HEADER ISOMERASE 03-OCT-24 9GYY TITLE CRYSTAL STRUCTURE OF DOMAIN-OF-UNKNOWN-FUNCTION DUF4867 FROM BACILLUS TITLE 2 MEGATERIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF4867 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PRIESTIA MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 GENE: BMQ_3647; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS SULFOQUINOVOSE; SULFOGLYCOLYSIS; SULFOSUGAR, DOMAIN-OF-UNKNOWN- KEYWDS 2 FUNCTION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SHARMA,G.J.DAVIES REVDAT 2 02-APR-25 9GYY 1 JRNL REVDAT 1 26-FEB-25 9GYY 0 JRNL AUTH M.SHARMA,N.PUDLO,M.A.JARVA,A.KAUR,A.JOHN,L.BURCHILL, JRNL AUTH 2 J.P.LINGFORD,R.EPA,P.ABAYAKOON,N.E.SCOTT,J.P.TURKENBURG, JRNL AUTH 3 G.J.DAVIES,E.C.MARTENS,E.D.GODDARD-BORGER,S.J.WILLIAMS JRNL TITL SULFOGLYCOLYSIS SUSTAINS EUBACTERIUM RECTALE IN LOW-FIBER JRNL TITL 2 DIETS. JRNL REF J.BIOL.CHEM. V. 301 08320 2025 JRNL REFN ESSN 1083-351X JRNL PMID 39956340 JRNL DOI 10.1016/J.JBC.2025.108320 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 83301 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4373 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6076 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 308 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.35000 REMARK 3 B12 (A**2) : -0.05000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.065 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.073 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3661 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4986 ; 2.163 ; 1.817 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 6.361 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 4 ; 7.544 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;12.578 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 562 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2784 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1800 ; 2.174 ; 2.159 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2253 ; 2.974 ; 3.882 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1861 ; 3.326 ; 2.398 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): 5770 ; 5.310 ;25.890 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9GYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87735 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 66.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 20.80 REMARK 200 R MERGE FOR SHELL (I) : 1.10300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A CRYSTAL OF LIGAND-FREE B. MEGATERIUM REMARK 280 SQVD WAS GROWN USING A 60 MG ML-1 PROTEIN SOLUTION IN 50 MM TRIS REMARK 280 BUFFER PH 7.5 CONTAINING 300 MM NACL IN A DROP WITH 0.15 UL REMARK 280 PROTEIN: 0.15 UL MOTHER LIQUOR, THE LATTER COMPRISING 2.0 M REMARK 280 SODIUM CHLORIDE AND 10 % W/V PEG (POLYETHYLENE GLYCOL) 6,000., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.28733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.64367 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.64367 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.28733 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: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HOH A 470 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 A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 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 A 25 CE NZ REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 ASP A 51 CG OD1 OD2 REMARK 470 GLN A 52 CD OE1 NE2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 LYS A 138 NZ REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 LYS A 169 CE NZ REMARK 470 GLN A 180 CG CD OE1 NE2 REMARK 470 GLN A 204 CG CD OE1 NE2 REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 GLN B 5 CG CD OE1 NE2 REMARK 470 LYS B 8 CE NZ REMARK 470 ASP B 9 CG OD1 OD2 REMARK 470 LYS B 12 CD CE NZ REMARK 470 LYS B 23 CD CE NZ REMARK 470 LYS B 25 NZ REMARK 470 GLU B 122 CG CD OE1 OE2 REMARK 470 GLN B 180 CG CD OE1 NE2 REMARK 470 GLU B 201 CG CD OE1 OE2 REMARK 470 GLU B 203 CG CD OE1 OE2 REMARK 470 LYS B 208 CE NZ REMARK 470 GLU B 217 CG CD OE1 OE2 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 ASN A 129 O HOH A 401 2.19 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 HIS A 26 CE1 HIS A 26 NE2 -0.067 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 MET A 62 CG - SD - CE ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG A 182 CG - CD - NE ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 182 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 182 CB - CG - CD ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG B 182 CG - CD - NE ANGL. DEV. = -22.0 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 ALA A 74 -66.06 -105.08 REMARK 500 GLU A 78 9.45 83.39 REMARK 500 ASN A 94 -43.86 72.61 REMARK 500 LYS A 100 51.52 -94.82 REMARK 500 PHE A 151 -150.59 -159.84 REMARK 500 ASN A 172 2.33 80.17 REMARK 500 ALA B 74 -68.03 -103.91 REMARK 500 GLU B 78 6.91 81.02 REMARK 500 ASN B 94 -50.68 76.84 REMARK 500 LYS B 100 52.02 -92.23 REMARK 500 PHE B 151 -155.21 -159.13 REMARK 500 PHE B 190 -38.92 -134.30 REMARK 500 REMARK 500 REMARK: NULL 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 97 OE2 REMARK 620 2 HIS A 99 NE2 93.5 REMARK 620 3 GLU A 103 OE1 173.3 83.6 REMARK 620 4 HIS A 150 NE2 97.9 102.2 88.6 REMARK 620 5 HOH A 432 O 92.9 165.0 88.6 90.3 REMARK 620 6 HOH A 504 O 83.3 90.0 90.7 167.5 77.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 209 O REMARK 620 2 HOH A 467 O 83.4 REMARK 620 3 HOH A 532 O 98.8 79.6 REMARK 620 4 ASP B 51 OD2 127.4 47.9 91.6 REMARK 620 5 HOH B 412 O 71.7 144.2 79.3 160.3 REMARK 620 6 HOH B 554 O 90.8 99.7 170.2 81.0 105.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 556 O REMARK 620 2 GLU B 33 OE2 131.4 REMARK 620 N 1 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 97 OE1 REMARK 620 2 HIS B 99 NE2 90.7 REMARK 620 3 GLU B 103 OE1 169.9 84.8 REMARK 620 4 HIS B 150 NE2 100.6 102.0 89.2 REMARK 620 5 HOH B 430 O 94.3 167.4 88.4 88.5 REMARK 620 6 HOH B 470 O 78.4 91.5 92.6 166.4 78.1 REMARK 620 N 1 2 3 4 5 DBREF 9GYY A 1 223 UNP D5E1T1 D5E1T1_PRIM1 1 223 DBREF 9GYY B 1 223 UNP D5E1T1 D5E1T1_PRIM1 1 223 SEQADV 9GYY MET A -19 UNP D5E1T1 INITIATING METHIONINE SEQADV 9GYY GLY A -18 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER A -17 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER A -16 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -15 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -14 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -13 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -12 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -11 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A -10 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER A -9 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER A -8 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY GLY A -7 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY LEU A -6 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY VAL A -5 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY PRO A -4 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY ARG A -3 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY GLY A -2 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER A -1 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS A 0 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY MET B -19 UNP D5E1T1 INITIATING METHIONINE SEQADV 9GYY GLY B -18 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER B -17 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER B -16 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -15 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -14 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -13 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -12 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -11 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B -10 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER B -9 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER B -8 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY GLY B -7 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY LEU B -6 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY VAL B -5 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY PRO B -4 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY ARG B -3 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY GLY B -2 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY SER B -1 UNP D5E1T1 EXPRESSION TAG SEQADV 9GYY HIS B 0 UNP D5E1T1 EXPRESSION TAG SEQRES 1 A 243 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 243 LEU VAL PRO ARG GLY SER HIS MET GLY SER PHE GLN TYR SEQRES 3 A 243 MET LYS ASP LEU ASN LYS HIS ILE PRO PHE TYR HIS ILE SEQRES 4 A 243 GLU ASP SER LYS PHE LYS HIS TYR GLY LYS VAL ILE ASN SEQRES 5 A 243 GLU TYR ASP PHE ASN GLU LEU GLU THR TYR MET ASP SER SEQRES 6 A 243 LEU THR ILE PRO GLN ASP GLN ASN VAL TYR VAL ALA SER SEQRES 7 A 243 VAL THR GLU MET GLU ASN THR ILE ILE LYS ASN GLN LEU SEQRES 8 A 243 GLN GLU ALA PHE TYR GLY GLU MET SER ILE GLN ILE GLY SEQRES 9 A 243 TYR CYS ASN GLY PRO ASN SER THR LEU ASN GLY LEU GLU SEQRES 10 A 243 TYR HIS LYS SER SER GLU ILE ASN ILE ALA ILE THR ASP SEQRES 11 A 243 MET VAL LEU LEU LEU GLY LYS VAL GLN GLU VAL GLU ASN SEQRES 12 A 243 ASN VAL PHE HIS SER ASN ASP VAL ILE ALA PHE PHE VAL SEQRES 13 A 243 PRO LYS GLY THR ALA VAL GLU LEU TYR SER THR THR LEU SEQRES 14 A 243 HIS PHE ALA PRO CYS LYS VAL ASN ASN GLU GLY PHE LYS SEQRES 15 A 243 THR ILE VAL ILE LEU PRO LYS GLY THR ASN ASP PRO LEU SEQRES 16 A 243 SER THR ASN ILE GLN LYS ARG THR LYS GLU ASP GLU LEU SEQRES 17 A 243 LEU PHE MET LYS ASN LYS TRP LEU ILE ALA HIS PRO GLU SEQRES 18 A 243 ARG GLU GLN LEU ILE ASN LYS GLY ALA HIS PRO GLY ILE SEQRES 19 A 243 LYS GLY GLU ASN ILE LYS VAL TYR GLN SEQRES 1 B 243 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 243 LEU VAL PRO ARG GLY SER HIS MET GLY SER PHE GLN TYR SEQRES 3 B 243 MET LYS ASP LEU ASN LYS HIS ILE PRO PHE TYR HIS ILE SEQRES 4 B 243 GLU ASP SER LYS PHE LYS HIS TYR GLY LYS VAL ILE ASN SEQRES 5 B 243 GLU TYR ASP PHE ASN GLU LEU GLU THR TYR MET ASP SER SEQRES 6 B 243 LEU THR ILE PRO GLN ASP GLN ASN VAL TYR VAL ALA SER SEQRES 7 B 243 VAL THR GLU MET GLU ASN THR ILE ILE LYS ASN GLN LEU SEQRES 8 B 243 GLN GLU ALA PHE TYR GLY GLU MET SER ILE GLN ILE GLY SEQRES 9 B 243 TYR CYS ASN GLY PRO ASN SER THR LEU ASN GLY LEU GLU SEQRES 10 B 243 TYR HIS LYS SER SER GLU ILE ASN ILE ALA ILE THR ASP SEQRES 11 B 243 MET VAL LEU LEU LEU GLY LYS VAL GLN GLU VAL GLU ASN SEQRES 12 B 243 ASN VAL PHE HIS SER ASN ASP VAL ILE ALA PHE PHE VAL SEQRES 13 B 243 PRO LYS GLY THR ALA VAL GLU LEU TYR SER THR THR LEU SEQRES 14 B 243 HIS PHE ALA PRO CYS LYS VAL ASN ASN GLU GLY PHE LYS SEQRES 15 B 243 THR ILE VAL ILE LEU PRO LYS GLY THR ASN ASP PRO LEU SEQRES 16 B 243 SER THR ASN ILE GLN LYS ARG THR LYS GLU ASP GLU LEU SEQRES 17 B 243 LEU PHE MET LYS ASN LYS TRP LEU ILE ALA HIS PRO GLU SEQRES 18 B 243 ARG GLU GLN LEU ILE ASN LYS GLY ALA HIS PRO GLY ILE SEQRES 19 B 243 LYS GLY GLU ASN ILE LYS VAL TYR GLN HET FE A 301 1 HET NA A 302 1 HET NA A 303 1 HET CL A 304 1 HET FE B 301 1 HETNAM FE FE (III) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 3 FE 2(FE 3+) FORMUL 4 NA 2(NA 1+) FORMUL 6 CL CL 1- FORMUL 8 HOH *387(H2 O) HELIX 1 AA1 GLY A 2 ASN A 11 1 10 HELIX 2 AA2 ASP A 21 HIS A 26 5 6 HELIX 3 AA3 PHE A 36 SER A 45 1 10 HELIX 4 AA4 VAL A 59 ASN A 64 1 6 HELIX 5 AA5 THR A 65 ALA A 74 1 10 HELIX 6 AA6 GLN A 119 VAL A 121 5 3 HELIX 7 AA7 ASN A 129 VAL A 131 5 3 HELIX 8 AA8 THR A 183 LEU A 188 1 6 HELIX 9 AA9 ARG A 202 ASN A 207 1 6 HELIX 10 AB1 SER B 3 ASN B 11 1 9 HELIX 11 AB2 ASP B 21 HIS B 26 5 6 HELIX 12 AB3 PHE B 36 SER B 45 1 10 HELIX 13 AB4 VAL B 59 ASN B 64 1 6 HELIX 14 AB5 THR B 65 ALA B 74 1 10 HELIX 15 AB6 GLN B 119 VAL B 121 5 3 HELIX 16 AB7 ASN B 129 VAL B 131 5 3 HELIX 17 AB8 LYS B 184 GLU B 187 5 4 HELIX 18 AB9 ARG B 202 ASN B 207 1 6 SHEET 1 AA1 4 PHE A 16 HIS A 18 0 SHEET 2 AA1 4 ILE A 132 VAL A 136 1 O PHE A 135 N TYR A 17 SHEET 3 AA1 4 MET A 111 LYS A 117 -1 N MET A 111 O VAL A 136 SHEET 4 AA1 4 THR A 148 LEU A 149 -1 O LEU A 149 N GLY A 116 SHEET 1 AA2 4 PHE A 16 HIS A 18 0 SHEET 2 AA2 4 ILE A 132 VAL A 136 1 O PHE A 135 N TYR A 17 SHEET 3 AA2 4 MET A 111 LYS A 117 -1 N MET A 111 O VAL A 136 SHEET 4 AA2 4 CYS A 154 LYS A 155 -1 O CYS A 154 N VAL A 112 SHEET 1 AA3 6 GLY A 28 ILE A 31 0 SHEET 2 AA3 6 ALA A 141 LEU A 144 -1 O GLU A 143 N LYS A 29 SHEET 3 AA3 6 GLU A 103 ALA A 107 -1 N GLU A 103 O LEU A 144 SHEET 4 AA3 6 PHE A 161 PRO A 168 -1 O ILE A 164 N ILE A 106 SHEET 5 AA3 6 ILE A 81 GLY A 88 -1 N GLN A 82 O LEU A 167 SHEET 6 AA3 6 VAL A 54 VAL A 56 -1 N VAL A 54 O ASN A 87 SHEET 1 AA4 3 GLY A 95 TYR A 98 0 SHEET 2 AA4 3 LYS A 194 ALA A 198 -1 O ILE A 197 N LEU A 96 SHEET 3 AA4 3 LEU A 189 MET A 191 -1 N PHE A 190 O LYS A 194 SHEET 1 AA5 3 GLY A 95 TYR A 98 0 SHEET 2 AA5 3 LYS A 194 ALA A 198 -1 O ILE A 197 N LEU A 96 SHEET 3 AA5 3 HIS A 211 PRO A 212 1 O HIS A 211 N ALA A 198 SHEET 1 AA6 2 PHE A 126 HIS A 127 0 SHEET 2 AA6 2 ILE A 214 LYS A 215 1 O LYS A 215 N PHE A 126 SHEET 1 AA7 4 PHE B 16 HIS B 18 0 SHEET 2 AA7 4 ILE B 132 VAL B 136 1 O ALA B 133 N TYR B 17 SHEET 3 AA7 4 MET B 111 LYS B 117 -1 N MET B 111 O VAL B 136 SHEET 4 AA7 4 THR B 148 LEU B 149 -1 O LEU B 149 N GLY B 116 SHEET 1 AA8 4 PHE B 16 HIS B 18 0 SHEET 2 AA8 4 ILE B 132 VAL B 136 1 O ALA B 133 N TYR B 17 SHEET 3 AA8 4 MET B 111 LYS B 117 -1 N MET B 111 O VAL B 136 SHEET 4 AA8 4 CYS B 154 LYS B 155 -1 O CYS B 154 N VAL B 112 SHEET 1 AA9 6 GLY B 28 ILE B 31 0 SHEET 2 AA9 6 ALA B 141 LEU B 144 -1 O GLU B 143 N LYS B 29 SHEET 3 AA9 6 GLU B 103 ALA B 107 -1 N GLU B 103 O LEU B 144 SHEET 4 AA9 6 PHE B 161 PRO B 168 -1 O ILE B 166 N ILE B 104 SHEET 5 AA9 6 ILE B 81 GLY B 88 -1 N GLN B 82 O LEU B 167 SHEET 6 AA9 6 VAL B 54 VAL B 56 -1 N VAL B 54 O ASN B 87 SHEET 1 AB1 3 GLY B 95 TYR B 98 0 SHEET 2 AB1 3 LYS B 194 ALA B 198 -1 O ILE B 197 N LEU B 96 SHEET 3 AB1 3 LEU B 189 MET B 191 -1 N PHE B 190 O LYS B 194 SHEET 1 AB2 3 GLY B 95 TYR B 98 0 SHEET 2 AB2 3 LYS B 194 ALA B 198 -1 O ILE B 197 N LEU B 96 SHEET 3 AB2 3 HIS B 211 PRO B 212 1 O HIS B 211 N ALA B 198 SHEET 1 AB3 2 PHE B 126 HIS B 127 0 SHEET 2 AB3 2 ILE B 214 LYS B 215 1 O LYS B 215 N PHE B 126 LINK OE2 GLU A 97 FE FE A 301 1555 1555 2.15 LINK NE2 HIS A 99 FE FE A 301 1555 1555 2.18 LINK OE1 GLU A 103 FE FE A 301 1555 1555 2.08 LINK NE2 HIS A 150 FE FE A 301 1555 1555 2.19 LINK O GLY A 209 NA NA A 302 1555 1555 2.35 LINK FE FE A 301 O HOH A 432 1555 1555 2.24 LINK FE FE A 301 O HOH A 504 1555 1555 2.17 LINK NA NA A 302 O HOH A 467 1555 1555 2.50 LINK NA NA A 302 O HOH A 532 1555 1555 2.35 LINK NA NA A 302 OD2 ASP B 51 2654 1555 2.53 LINK NA NA A 302 O HOH B 412 1555 3665 2.37 LINK NA NA A 302 O HOH B 554 1555 3665 2.30 LINK NA NA A 303 O HOH A 556 1555 1555 3.16 LINK NA NA A 303 OE2 GLU B 33 1555 1555 2.23 LINK OE1 GLU B 97 FE FE B 301 1555 1555 2.32 LINK NE2 HIS B 99 FE FE B 301 1555 1555 2.17 LINK OE1 GLU B 103 FE FE B 301 1555 1555 2.06 LINK NE2 HIS B 150 FE FE B 301 1555 1555 2.15 LINK FE FE B 301 O HOH B 430 1555 1555 2.30 LINK FE FE B 301 O HOH B 470 1555 1555 2.03 CRYST1 83.835 83.835 133.931 90.00 90.00 120.00 P 32 2 1 12 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 0.011928 0.006887 0.000000 0.00000 SCALE2 0.000000 0.013773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007467 0.00000 CONECT 784 3570 CONECT 806 3570 CONECT 835 3570 CONECT 1206 3570 CONECT 1679 3571 CONECT 2046 3572 CONECT 2557 3574 CONECT 2580 3574 CONECT 2609 3574 CONECT 2981 3574 CONECT 3570 784 806 835 1206 CONECT 3570 3606 3678 CONECT 3571 1679 3641 3706 CONECT 3572 2046 3730 CONECT 3574 2557 2580 2609 2981 CONECT 3574 3793 3833 CONECT 3606 3570 CONECT 3641 3571 CONECT 3678 3570 CONECT 3706 3571 CONECT 3730 3572 CONECT 3793 3574 CONECT 3833 3574 MASTER 463 0 5 18 44 0 0 6 3901 2 23 38 END