HEADER OXIDOREDUCTASE 02-JUL-20 6ZMA TITLE STRUCTURE OF THE TRNA-MONOOXYGENASE ENZYME MIAE FROZEN UNDER 140 BAR TITLE 2 OF KRYPTON USING THE SOAK AND FREEZE METHODOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA HYDROXYLASE; COMPND 3 CHAIN: B, C; COMPND 4 SYNONYM: TRNA-(MS[2]IO[6]A)-HYDROXYLASE (MIAE),TRNA-(MS[2]IO[6]A)- COMPND 5 HYDROXYLASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: AYO08_21560, CBL13_00280, CBP06_18695; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS TRNA-MONOOXYGENASE METALLO-ENZYME TRNA-MODIFYING ENZYME HYDROXYLASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.CARPENTIER,M.ATTA REVDAT 3 31-JAN-24 6ZMA 1 REMARK REVDAT 2 07-OCT-20 6ZMA 1 JRNL REVDAT 1 02-SEP-20 6ZMA 0 JRNL AUTH P.CARPENTIER,C.LEPRETRE,C.BASSET,T.DOUKI,S.TORELLI,V.DUARTE, JRNL AUTH 2 D.HAMDANE,M.FONTECAVE,M.ATTA JRNL TITL STRUCTURAL, BIOCHEMICAL AND FUNCTIONAL ANALYSES OF JRNL TITL 2 TRNA-MONOOXYGENASE ENZYME MIAE FROM PSEUDOMONAS PUTIDA JRNL TITL 3 PROVIDE INSIGHTS INTO TRNA/MIAE INTERACTION. JRNL REF NUCLEIC ACIDS RES. V. 48 9918 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32785618 JRNL DOI 10.1093/NAR/GKAA667 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 23939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1290 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1185 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3131 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.27000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : 1.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.535 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3288 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3234 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4425 ; 1.435 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7403 ; 0.977 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 406 ; 5.489 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;33.152 ;22.897 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;17.038 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3643 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 736 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 REFINED INDIVIDUALLY REMARK 3 KR ATOMS (LOW OCCUPANCIES) HAVE BEEN LOCATED IN ANOMALOUS MAP REMARK 4 REMARK 4 6ZMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8610 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25240 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2ITB REMARK 200 REMARK 200 REMARK: ELONGATED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MIAE:20 MG/ML IN 100 MM HEPES, PH 7.5, REMARK 280 30 MM NACL RESERVOIR SOLUTION: 0.5 M CACL2, 42% PEG 6K, 2 M TRIS- REMARK 280 CL PH 8 FROZEN UNDER 140 BAR OF KRYPTON KRYPTON ATOMS WERE REMARK 280 LOCATED IN ANOMALOUS MAP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.81100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.81100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA B 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 421 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 444 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 479 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 480 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ALA B 202 REMARK 465 LEU B 203 REMARK 465 ALA B 204 REMARK 465 ALA B 205 REMARK 465 MET C 1 REMARK 465 GLN C 201 REMARK 465 ALA C 202 REMARK 465 LEU C 203 REMARK 465 ALA C 204 REMARK 465 ALA C 205 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 51 NZ REMARK 470 ARG B 101 CD NE CZ NH1 NH2 REMARK 470 ARG B 142 CD NE CZ NH1 NH2 REMARK 470 ARG B 174 NE CZ NH1 NH2 REMARK 470 GLN B 191 CB CG CD OE1 NE2 REMARK 470 ARG C 78 NH1 NH2 REMARK 470 GLU C 168 OE1 OE2 REMARK 470 ARG C 173 CD NE CZ NH1 NH2 REMARK 470 ARG C 174 CZ NH1 NH2 REMARK 470 SER C 188 OG REMARK 470 GLN C 191 CB CG CD OE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 51 CD CE REMARK 480 ARG B 78 NE CZ NH1 NH2 REMARK 480 LYS B 81 CD CE NZ REMARK 480 LYS B 149 CG CD CE REMARK 480 ASP B 170 CG OD1 OD2 REMARK 480 SER C 2 OG REMARK 480 LYS C 51 CD CE REMARK 480 ARG C 82 NH1 NH2 REMARK 480 HIS C 106 CB CG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 425 O HOH C 438 1.13 REMARK 500 OH TYR C 144 KR KR C 310 1.29 REMARK 500 O PRO C 200 O HOH C 401 1.32 REMARK 500 NH2 ARG B 78 O HOH B 401 1.36 REMARK 500 CZ ARG C 78 O HOH C 411 1.42 REMARK 500 CB ASP B 167 OD2 ASP B 170 1.51 REMARK 500 CA GLN B 191 O HOH B 402 1.60 REMARK 500 O HOH C 410 O HOH C 412 1.73 REMARK 500 O2 PEG C 305 O HOH C 402 1.78 REMARK 500 N GLN B 191 O HOH B 402 1.80 REMARK 500 CG ASP B 167 OD2 ASP B 170 1.81 REMARK 500 O HOH B 473 O HOH B 485 1.82 REMARK 500 OD2 ASP B 167 OD2 ASP B 170 1.82 REMARK 500 C PRO C 200 O HOH C 401 1.84 REMARK 500 NH1 ARG B 78 C2 EDO B 313 1.84 REMARK 500 O HOH C 404 O HOH C 485 1.92 REMARK 500 CZ TYR C 144 KR KR C 310 1.95 REMARK 500 O HOH B 451 O HOH B 456 1.98 REMARK 500 O GLY B 166 O HOH B 404 2.06 REMARK 500 CZ ARG B 78 O HOH B 401 2.06 REMARK 500 O HOH B 465 O HOH B 487 2.08 REMARK 500 NZ LYS C 40 O HOH C 403 2.12 REMARK 500 OE1 GLU C 122 OE2 GLU C 151 2.14 REMARK 500 OG1 THR B 54 O HOH B 405 2.15 REMARK 500 O1 EDO C 313 O HOH C 404 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 425 O HOH C 446 4546 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 78 CD ARG B 78 NE -0.470 REMARK 500 ARG B 78 NE ARG B 78 CZ -0.145 REMARK 500 ARG B 78 CZ ARG B 78 NH1 -0.140 REMARK 500 ARG B 78 CZ ARG B 78 NH2 -0.123 REMARK 500 LYS B 81 CG LYS B 81 CD -0.624 REMARK 500 LYS B 81 CE LYS B 81 NZ -0.188 REMARK 500 LYS B 149 CB LYS B 149 CG -0.234 REMARK 500 LYS B 149 CD LYS B 149 CE -0.608 REMARK 500 LYS B 149 CE LYS B 149 NZ -1.270 REMARK 500 ASP B 170 CB ASP B 170 CG -0.155 REMARK 500 ASP B 170 CG ASP B 170 OD1 -0.187 REMARK 500 ASP B 170 CG ASP B 170 OD2 -0.141 REMARK 500 LYS C 51 CG LYS C 51 CD -0.359 REMARK 500 LYS C 51 CD LYS C 51 CE -0.311 REMARK 500 LYS C 51 CE LYS C 51 NZ -0.657 REMARK 500 ARG C 82 CZ ARG C 82 NH2 -0.573 REMARK 500 HIS C 106 CG HIS C 106 CD2 -0.102 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS B 51 CB - CG - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG B 78 CG - CD - NE ANGL. DEV. = 26.1 DEGREES REMARK 500 ARG B 78 CD - NE - CZ ANGL. DEV. = 24.9 DEGREES REMARK 500 LYS B 81 CB - CG - CD ANGL. DEV. = 27.6 DEGREES REMARK 500 LYS B 81 CG - CD - CE ANGL. DEV. = 33.6 DEGREES REMARK 500 LYS B 149 CB - CG - CD ANGL. DEV. = 25.1 DEGREES REMARK 500 ASP B 170 CA - CB - CG ANGL. DEV. = 20.7 DEGREES REMARK 500 ASP B 170 CB - CG - OD1 ANGL. DEV. = -54.1 DEGREES REMARK 500 ASP B 170 CB - CG - OD2 ANGL. DEV. = 46.3 DEGREES REMARK 500 LYS C 51 CG - CD - CE ANGL. DEV. = 48.0 DEGREES REMARK 500 LYS C 51 CD - CE - NZ ANGL. DEV. = 32.3 DEGREES REMARK 500 ARG C 82 NH1 - CZ - NH2 ANGL. DEV. = 35.7 DEGREES REMARK 500 ARG C 82 NE - CZ - NH1 ANGL. DEV. = -36.6 DEGREES REMARK 500 ARG C 82 NE - CZ - NH2 ANGL. DEV. = -36.8 DEGREES REMARK 500 HIS C 106 CB - CG - CD2 ANGL. DEV. = -10.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR B 52 51.04 -107.98 REMARK 500 ASP B 167 63.72 81.50 REMARK 500 ILE C 4 80.34 54.80 REMARK 500 TYR C 52 53.89 -111.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 166 ASP B 167 31.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 515 DISTANCE = 6.33 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 O REMARK 620 2 LEU B 11 O 87.6 REMARK 620 3 HOH B 432 O 89.5 95.0 REMARK 620 4 ASP C 8 O 53.2 38.0 107.5 REMARK 620 5 LEU C 11 O 55.9 35.4 107.6 2.7 REMARK 620 6 HOH C 419 O 93.3 85.4 177.2 74.4 74.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 38 OE1 REMARK 620 2 GLU B 69 OE2 86.1 REMARK 620 3 HIS B 72 ND1 91.6 94.4 REMARK 620 4 TRS B 306 O3 90.3 88.9 176.3 REMARK 620 5 HOH B 407 O 94.2 176.5 89.1 87.6 REMARK 620 6 HOH B 445 O 172.0 99.8 93.2 84.6 79.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 69 OE1 REMARK 620 2 GLU B 122 OE1 90.2 REMARK 620 3 GLU B 151 OE2 154.9 75.1 REMARK 620 4 HIS B 154 ND1 92.1 87.0 107.1 REMARK 620 5 TRS B 306 O2 102.8 58.8 52.2 142.1 REMARK 620 6 TRS B 306 O3 84.0 113.1 83.2 159.5 58.0 REMARK 620 7 HOH B 445 O 119.8 147.0 80.5 79.2 120.1 85.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 422 O REMARK 620 2 HOH B 422 O 167.1 REMARK 620 3 HOH B 444 O 83.6 83.6 REMARK 620 4 HOH B 444 O 83.6 83.6 0.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 38 OE1 REMARK 620 2 GLU C 69 OE1 86.8 REMARK 620 3 HIS C 72 ND1 98.8 99.7 REMARK 620 4 TRS C 303 O1 84.9 83.3 175.3 REMARK 620 5 HOH C 421 O 90.0 170.0 90.2 87.0 REMARK 620 6 HOH C 457 O 166.6 95.5 93.8 82.3 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 69 OE2 REMARK 620 2 GLU C 122 OE1 125.0 REMARK 620 3 GLU C 122 OE2 76.2 48.9 REMARK 620 4 GLU C 151 OE2 161.5 51.1 96.6 REMARK 620 5 HIS C 154 ND1 85.4 93.6 92.5 112.2 REMARK 620 6 TRS C 303 O1 87.7 110.2 109.3 78.6 154.8 REMARK 620 7 HOH C 457 O 111.9 121.7 166.9 78.7 78.3 81.9 REMARK 620 N 1 2 3 4 5 6 DBREF1 6ZMA B 1 205 UNP A0A179QS89_PSEPU DBREF2 6ZMA B A0A179QS89 1 205 DBREF1 6ZMA C 1 205 UNP A0A179QS89_PSEPU DBREF2 6ZMA C A0A179QS89 1 205 SEQRES 1 B 205 MET SER LEU ILE PRO GLU ILE ASP ALA PHE LEU GLY CYS SEQRES 2 B 205 PRO THR PRO ASP ALA TRP ILE GLU ALA ALA LEU ALA ASP SEQRES 3 B 205 GLN GLU THR LEU LEU ILE ASP HIS LYS ASN CYS GLU PHE SEQRES 4 B 205 LYS ALA ALA SER THR ALA LEU SER LEU ILE ALA LYS TYR SEQRES 5 B 205 ASN THR HIS LEU ASP LEU ILE ASN MET MET SER ARG LEU SEQRES 6 B 205 ALA ARG GLU GLU LEU VAL HIS HIS GLU GLN VAL LEU ARG SEQRES 7 B 205 LEU MET LYS ARG ARG GLY VAL PRO LEU ARG PRO VAL SER SEQRES 8 B 205 ALA GLY ARG TYR ALA SER GLY LEU ARG ARG LEU VAL ARG SEQRES 9 B 205 ALA HIS GLU PRO VAL LYS LEU VAL ASP THR LEU VAL VAL SEQRES 10 B 205 GLY ALA PHE ILE GLU ALA ARG SER CYS GLU ARG PHE ALA SEQRES 11 B 205 ALA LEU VAL PRO HIS LEU ASP GLU GLU LEU GLY ARG PHE SEQRES 12 B 205 TYR HIS GLY LEU LEU LYS SER GLU ALA ARG HIS TYR GLN SEQRES 13 B 205 GLY TYR LEU LYS LEU ALA HIS ASN TYR GLY ASP GLU ALA SEQRES 14 B 205 ASP ILE ALA ARG ARG VAL GLU LEU VAL ARG ALA ALA GLU SEQRES 15 B 205 MET GLU LEU ILE GLN SER PRO ASP GLN GLU LEU ARG PHE SEQRES 16 B 205 HIS SER GLY ILE PRO GLN ALA LEU ALA ALA SEQRES 1 C 205 MET SER LEU ILE PRO GLU ILE ASP ALA PHE LEU GLY CYS SEQRES 2 C 205 PRO THR PRO ASP ALA TRP ILE GLU ALA ALA LEU ALA ASP SEQRES 3 C 205 GLN GLU THR LEU LEU ILE ASP HIS LYS ASN CYS GLU PHE SEQRES 4 C 205 LYS ALA ALA SER THR ALA LEU SER LEU ILE ALA LYS TYR SEQRES 5 C 205 ASN THR HIS LEU ASP LEU ILE ASN MET MET SER ARG LEU SEQRES 6 C 205 ALA ARG GLU GLU LEU VAL HIS HIS GLU GLN VAL LEU ARG SEQRES 7 C 205 LEU MET LYS ARG ARG GLY VAL PRO LEU ARG PRO VAL SER SEQRES 8 C 205 ALA GLY ARG TYR ALA SER GLY LEU ARG ARG LEU VAL ARG SEQRES 9 C 205 ALA HIS GLU PRO VAL LYS LEU VAL ASP THR LEU VAL VAL SEQRES 10 C 205 GLY ALA PHE ILE GLU ALA ARG SER CYS GLU ARG PHE ALA SEQRES 11 C 205 ALA LEU VAL PRO HIS LEU ASP GLU GLU LEU GLY ARG PHE SEQRES 12 C 205 TYR HIS GLY LEU LEU LYS SER GLU ALA ARG HIS TYR GLN SEQRES 13 C 205 GLY TYR LEU LYS LEU ALA HIS ASN TYR GLY ASP GLU ALA SEQRES 14 C 205 ASP ILE ALA ARG ARG VAL GLU LEU VAL ARG ALA ALA GLU SEQRES 15 C 205 MET GLU LEU ILE GLN SER PRO ASP GLN GLU LEU ARG PHE SEQRES 16 C 205 HIS SER GLY ILE PRO GLN ALA LEU ALA ALA HET FE B 301 1 HET FE B 302 1 HET CL B 303 1 HET CA B 304 1 HET CA B 305 1 HET TRS B 306 8 HET PEG B 307 7 HET PEG B 308 7 HET PEG B 309 7 HET PG4 B 310 13 HET KR B 311 1 HET KR B 312 1 HET EDO B 313 4 HET FE C 301 1 HET FE C 302 1 HET TRS C 303 8 HET PEG C 304 7 HET PEG C 305 7 HET PEG C 306 7 HET PEG C 307 7 HET KR C 308 1 HET KR C 309 1 HET KR C 310 1 HET KR C 311 1 HET EDO C 312 4 HET EDO C 313 4 HETNAM FE FE (III) ION HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM KR KRYPTON HETNAM EDO 1,2-ETHANEDIOL HETSYN TRS TRIS BUFFER HETSYN EDO ETHYLENE GLYCOL FORMUL 3 FE 4(FE 3+) FORMUL 5 CL CL 1- FORMUL 6 CA 2(CA 2+) FORMUL 8 TRS 2(C4 H12 N O3 1+) FORMUL 9 PEG 7(C4 H10 O3) FORMUL 12 PG4 C8 H18 O5 FORMUL 13 KR 6(KR) FORMUL 15 EDO 3(C2 H6 O2) FORMUL 29 HOH *212(H2 O) HELIX 1 AA1 GLU B 6 LEU B 11 1 6 HELIX 2 AA2 PRO B 16 ALA B 25 1 10 HELIX 3 AA3 ASP B 26 TYR B 52 1 27 HELIX 4 AA4 HIS B 55 ARG B 83 1 29 HELIX 5 AA5 ARG B 94 LEU B 102 1 9 HELIX 6 AA6 PRO B 108 VAL B 133 1 26 HELIX 7 AA7 PRO B 134 LEU B 136 5 3 HELIX 8 AA8 ASP B 137 TYR B 165 1 29 HELIX 9 AA9 ASP B 167 SER B 188 1 22 HELIX 10 AB1 GLU C 6 LEU C 11 1 6 HELIX 11 AB2 PRO C 16 ASP C 26 1 11 HELIX 12 AB3 ASP C 26 TYR C 52 1 27 HELIX 13 AB4 HIS C 55 ARG C 83 1 29 HELIX 14 AB5 ARG C 94 ARG C 101 1 8 HELIX 15 AB6 PRO C 108 VAL C 133 1 26 HELIX 16 AB7 PRO C 134 LEU C 136 5 3 HELIX 17 AB8 ASP C 137 TYR C 165 1 29 HELIX 18 AB9 ASP C 167 SER C 188 1 22 LINK O ASP B 8 CA CA B 304 1555 1555 2.30 LINK O LEU B 11 CA CA B 304 1555 1555 2.34 LINK OE1 GLU B 38 FE FE B 301 1555 1555 2.12 LINK OE2 GLU B 69 FE FE B 301 1555 1555 2.23 LINK OE1 GLU B 69 FE FE B 302 1555 1555 2.51 LINK ND1 HIS B 72 FE FE B 301 1555 1555 2.46 LINK OE1 GLU B 122 FE FE B 302 1555 1555 2.41 LINK OE2 GLU B 151 FE FE B 302 1555 1555 2.73 LINK ND1 HIS B 154 FE FE B 302 1555 1555 2.47 LINK FE FE B 301 O3 TRS B 306 1555 1555 2.12 LINK FE FE B 301 O HOH B 407 1555 1555 2.33 LINK FE FE B 301 O HOH B 445 1555 1555 2.47 LINK FE FE B 302 O2 TRS B 306 1555 1555 2.64 LINK FE FE B 302 O3 TRS B 306 1555 1555 2.37 LINK FE FE B 302 O HOH B 445 1555 1555 2.20 LINK CA CA B 304 O HOH B 432 1555 1555 2.38 LINK CA CA B 304 O ASP C 8 3545 1555 2.30 LINK CA CA B 304 O LEU C 11 3545 1555 2.34 LINK CA CA B 304 O HOH C 419 1555 3455 2.26 LINK CA CA B 305 O HOH B 422 1555 1555 2.57 LINK CA CA B 305 O HOH B 422 1555 2555 2.57 LINK CA CA B 305 O HOH B 444 1555 1555 2.38 LINK CA CA B 305 O HOH B 444 1555 2555 2.38 LINK OE1 GLU C 38 FE FE C 301 1555 1555 2.22 LINK OE1 GLU C 69 FE FE C 301 1555 1555 2.08 LINK OE2 GLU C 69 FE FE C 302 1555 1555 2.35 LINK ND1 HIS C 72 FE FE C 301 1555 1555 2.36 LINK OE1 GLU C 122 FE FE C 302 1555 1555 2.45 LINK OE2 GLU C 122 FE FE C 302 1555 1555 2.63 LINK OE2 GLU C 151 FE FE C 302 1555 1555 2.50 LINK ND1 HIS C 154 FE FE C 302 1555 1555 2.59 LINK FE FE C 301 O1 TRS C 303 1555 1555 2.19 LINK FE FE C 301 O HOH C 421 1555 1555 2.41 LINK FE FE C 301 O HOH C 457 1555 1555 2.38 LINK FE FE C 302 O1 TRS C 303 1555 1555 2.42 LINK FE FE C 302 O HOH C 457 1555 1555 2.17 CISPEP 1 GLU B 107 PRO B 108 0 5.90 CISPEP 2 GLU C 107 PRO C 108 0 1.06 CRYST1 117.622 52.300 79.407 90.00 90.74 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008502 0.000000 0.000109 0.00000 SCALE2 0.000000 0.019120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012594 0.00000