HEADER TRANSFERASE 10-NOV-16 5H62 TITLE STRUCTURE OF TRANSFERASE MUTANT-C23S,C199S COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.PARK,Y.YOO,J.KIM REVDAT 5 20-MAR-24 5H62 1 LINK REVDAT 4 31-OCT-18 5H62 1 JRNL REVDAT 3 24-OCT-18 5H62 1 JRNL REVDAT 2 19-SEP-18 5H62 1 JRNL REVDAT 1 27-DEC-17 5H62 0 JRNL AUTH J.B.PARK,Y.H.KIM,Y.YOO,J.KIM,S.H.JUN,J.W.CHO,S.EL QAIDI, JRNL AUTH 2 S.WALPOLE,S.MONACO,A.A.GARCIA-GARCIA,M.WU,M.P.HAYS, JRNL AUTH 3 R.HURTADO-GUERRERO,J.ANGULO,P.R.HARDWIDGE,J.S.SHIN,H.S.CHO JRNL TITL STRUCTURAL BASIS FOR ARGININE GLYCOSYLATION OF HOST JRNL TITL 2 SUBSTRATES BY BACTERIAL EFFECTOR PROTEINS. JRNL REF NAT COMMUN V. 9 4283 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30327479 JRNL DOI 10.1038/S41467-018-06680-6 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 77783 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4044 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5786 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 282 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4894 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 557 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5074 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4581 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6867 ; 1.997 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10681 ; 1.132 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 604 ; 6.268 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;35.710 ;24.843 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;13.808 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;21.923 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 731 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5599 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1014 ; 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): 2425 ; 2.773 ; 2.568 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2424 ; 2.772 ; 2.568 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3026 ; 3.817 ; 3.839 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3027 ; 3.818 ; 3.840 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2649 ; 4.145 ; 3.009 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2648 ; 4.146 ; 3.009 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3842 ; 6.021 ; 4.341 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 22200 ; 7.727 ;50.494 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 22201 ; 7.727 ;50.493 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5H62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS (PH 6.5), 0.005M MNCL2, REMARK 280 26% (W/V) PEG 3350, EVAPORATION, RECRYSTALLIZATION, TEMPERATURE REMARK 280 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 71.81500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 PHE A 4 REMARK 465 ASN A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 PHE A 8 REMARK 465 THR A 9 REMARK 465 ARG A 10 REMARK 465 ILE A 11 REMARK 465 LYS A 12 REMARK 465 ILE A 13 REMARK 465 MET A 14 REMARK 465 PHE A 15 REMARK 465 SER A 16 REMARK 465 ARG A 17 REMARK 465 ILE A 18 REMARK 465 ARG A 19 REMARK 465 GLY A 20 REMARK 465 LEU A 21 REMARK 465 ILE A 22 REMARK 465 SER A 23 REMARK 465 CYS A 24 REMARK 465 GLN A 25 REMARK 465 SER A 26 REMARK 465 ASN A 27 REMARK 465 THR A 28 REMARK 465 GLN A 29 REMARK 465 THR A 30 REMARK 465 ILE A 31 REMARK 465 ALA A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 LEU A 35 REMARK 465 SER A 36 REMARK 465 PRO A 37 REMARK 465 PRO A 38 REMARK 465 SER A 39 REMARK 465 LYS A 264 REMARK 465 ASP A 265 REMARK 465 ASN A 266 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ARG B 3 REMARK 465 PHE B 4 REMARK 465 ASN B 5 REMARK 465 ALA B 6 REMARK 465 ALA B 7 REMARK 465 PHE B 8 REMARK 465 THR B 9 REMARK 465 ARG B 10 REMARK 465 ILE B 11 REMARK 465 LYS B 12 REMARK 465 ILE B 13 REMARK 465 MET B 14 REMARK 465 PHE B 15 REMARK 465 SER B 16 REMARK 465 ARG B 17 REMARK 465 ILE B 18 REMARK 465 ARG B 19 REMARK 465 GLY B 20 REMARK 465 LEU B 21 REMARK 465 ILE B 22 REMARK 465 SER B 23 REMARK 465 CYS B 24 REMARK 465 GLN B 25 REMARK 465 SER B 26 REMARK 465 ASN B 27 REMARK 465 THR B 28 REMARK 465 GLN B 29 REMARK 465 THR B 30 REMARK 465 ILE B 31 REMARK 465 ALA B 32 REMARK 465 PRO B 33 REMARK 465 THR B 34 REMARK 465 LEU B 35 REMARK 465 SER B 36 REMARK 465 PRO B 37 REMARK 465 PRO B 38 REMARK 465 SER B 39 REMARK 465 SER B 40 REMARK 465 LEU B 342 REMARK 465 THR B 343 REMARK 465 ALA B 344 REMARK 465 SER B 345 REMARK 465 SER B 346 REMARK 465 TRP B 347 REMARK 465 ARG B 348 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 ND1 HIS B 200 O1 EDO B 401 1.90 REMARK 500 O HOH B 512 O HOH B 639 1.98 REMARK 500 O HOH A 518 O HOH A 559 2.00 REMARK 500 CD ARG A 128 O HOH A 579 2.07 REMARK 500 O HOH A 514 O HOH A 660 2.17 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 SER A 215 CB SER A 215 OG -0.124 REMARK 500 SER A 294 CB SER A 294 OG -0.101 REMARK 500 GLU B 165 CD GLU B 165 OE1 0.076 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 GLN A 58 CB - CA - C ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ASP A 204 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 204 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ASP A 246 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP A 320 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP B 111 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 117 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 216 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 326 CB - CG - OD1 ANGL. DEV. = 7.1 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 ASN A 82 54.62 -152.68 REMARK 500 GLU A 99 59.03 -94.19 REMARK 500 ASN A 185 95.66 -161.69 REMARK 500 THR A 343 -88.26 -129.72 REMARK 500 TRP A 347 -25.37 -144.30 REMARK 500 ASN B 82 52.36 -154.42 REMARK 500 GLU B 99 52.00 -99.16 REMARK 500 ASN B 185 68.59 -157.32 REMARK 500 LYS B 196 1.96 84.17 REMARK 500 ASP B 255 23.84 49.83 REMARK 500 TYR B 301 -64.85 -95.06 REMARK 500 TRP B 304 -72.72 -74.36 REMARK 500 ASP B 314 68.92 -153.19 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 LYS B 264 ASP B 265 -43.86 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 A 824 DISTANCE = 6.60 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 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 241 OD2 REMARK 620 2 ASN A 338 OD1 88.4 REMARK 620 3 SER A 340 OG 81.9 87.3 REMARK 620 4 UDP A 404 O2B 169.2 95.9 88.4 REMARK 620 5 UDP A 404 O1A 89.2 176.8 94.5 86.9 REMARK 620 6 HOH A 572 O 84.9 87.3 165.9 105.2 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 405 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 322 OD1 REMARK 620 2 HIS B 267 NE2 93.6 REMARK 620 3 SER B 269 OG 87.8 85.8 REMARK 620 4 HOH B 566 O 92.9 173.5 93.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 241 OD2 REMARK 620 2 SER B 340 OG 76.2 REMARK 620 3 UDP B 402 O1A 91.0 90.4 REMARK 620 4 UDP B 402 O1B 175.5 100.0 86.5 REMARK 620 5 HOH B 511 O 91.0 91.1 177.7 91.6 REMARK 620 6 HOH B 540 O 87.8 162.7 96.4 96.3 82.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H5Y RELATED DB: PDB REMARK 900 RELATED ID: 5H60 RELATED DB: PDB REMARK 900 RELATED ID: 5H61 RELATED DB: PDB REMARK 900 RELATED ID: 5H63 RELATED DB: PDB DBREF 5H62 A 1 348 PDB 5H62 5H62 1 348 DBREF 5H62 B 1 348 PDB 5H62 5H62 1 348 SEQRES 1 A 348 MET ALA ARG PHE ASN ALA ALA PHE THR ARG ILE LYS ILE SEQRES 2 A 348 MET PHE SER ARG ILE ARG GLY LEU ILE SER CYS GLN SER SEQRES 3 A 348 ASN THR GLN THR ILE ALA PRO THR LEU SER PRO PRO SER SEQRES 4 A 348 SER GLY HIS VAL SER PHE ALA GLY ILE ASP TYR PRO LEU SEQRES 5 A 348 LEU PRO LEU ASN HIS GLN THR PRO LEU VAL PHE GLN TRP SEQRES 6 A 348 PHE GLU ARG ASN PRO ASP ARG PHE GLY GLN ASN GLU ILE SEQRES 7 A 348 PRO ILE ILE ASN THR GLN LYS ASN PRO TYR LEU ASN ASN SEQRES 8 A 348 ILE ILE ASN ALA ALA ILE ILE GLU LYS GLU ARG ILE ILE SEQRES 9 A 348 GLY ILE PHE VAL ASP GLY ASP PHE SER LYS GLY GLN ARG SEQRES 10 A 348 LYS ALA LEU GLY LYS LEU GLU GLN ASN TYR ARG ASN ILE SEQRES 11 A 348 LYS VAL ILE TYR ASN SER ASP LEU ASN TYR SER MET TYR SEQRES 12 A 348 ASP LYS LYS LEU THR THR ILE TYR LEU GLU ASN ILE THR SEQRES 13 A 348 LYS LEU GLU ALA GLN SER ALA SER GLU ARG ASP GLU VAL SEQRES 14 A 348 LEU LEU ASN GLY VAL LYS LYS SER LEU GLU ASP VAL LEU SEQRES 15 A 348 LYS ASN ASN PRO GLU GLU THR LEU ILE SER SER HIS ASN SEQRES 16 A 348 LYS ASP LYS GLY HIS LEU TRP PHE ASP PHE TYR ARG ASN SEQRES 17 A 348 LEU PHE LEU LEU LYS GLY SER ASP ALA PHE LEU GLU ALA SEQRES 18 A 348 GLY LYS PRO GLY CYS HIS HIS LEU GLN PRO GLY GLY GLY SEQRES 19 A 348 CYS ILE TYR LEU ASP ALA ASP MET LEU LEU THR ASP LYS SEQRES 20 A 348 LEU GLY THR LEU TYR LEU PRO ASP GLY ILE ALA ILE HIS SEQRES 21 A 348 VAL SER ARG LYS ASP ASN HIS VAL SER LEU GLU ASN GLY SEQRES 22 A 348 ILE ILE ALA VAL ASN ARG SER GLU HIS PRO ALA LEU ILE SEQRES 23 A 348 LYS GLY LEU GLU ILE MET HIS SER LYS PRO TYR GLY ASP SEQRES 24 A 348 PRO TYR ASN ASP TRP LEU SER LYS GLY LEU ARG HIS TYR SEQRES 25 A 348 PHE ASP GLY SER HIS ILE GLN ASP TYR ASP ALA PHE CYS SEQRES 26 A 348 ASP PHE ILE GLU PHE LYS HIS GLU ASN ILE ILE MET ASN SEQRES 27 A 348 THR SER SER LEU THR ALA SER SER TRP ARG SEQRES 1 B 348 MET ALA ARG PHE ASN ALA ALA PHE THR ARG ILE LYS ILE SEQRES 2 B 348 MET PHE SER ARG ILE ARG GLY LEU ILE SER CYS GLN SER SEQRES 3 B 348 ASN THR GLN THR ILE ALA PRO THR LEU SER PRO PRO SER SEQRES 4 B 348 SER GLY HIS VAL SER PHE ALA GLY ILE ASP TYR PRO LEU SEQRES 5 B 348 LEU PRO LEU ASN HIS GLN THR PRO LEU VAL PHE GLN TRP SEQRES 6 B 348 PHE GLU ARG ASN PRO ASP ARG PHE GLY GLN ASN GLU ILE SEQRES 7 B 348 PRO ILE ILE ASN THR GLN LYS ASN PRO TYR LEU ASN ASN SEQRES 8 B 348 ILE ILE ASN ALA ALA ILE ILE GLU LYS GLU ARG ILE ILE SEQRES 9 B 348 GLY ILE PHE VAL ASP GLY ASP PHE SER LYS GLY GLN ARG SEQRES 10 B 348 LYS ALA LEU GLY LYS LEU GLU GLN ASN TYR ARG ASN ILE SEQRES 11 B 348 LYS VAL ILE TYR ASN SER ASP LEU ASN TYR SER MET TYR SEQRES 12 B 348 ASP LYS LYS LEU THR THR ILE TYR LEU GLU ASN ILE THR SEQRES 13 B 348 LYS LEU GLU ALA GLN SER ALA SER GLU ARG ASP GLU VAL SEQRES 14 B 348 LEU LEU ASN GLY VAL LYS LYS SER LEU GLU ASP VAL LEU SEQRES 15 B 348 LYS ASN ASN PRO GLU GLU THR LEU ILE SER SER HIS ASN SEQRES 16 B 348 LYS ASP LYS GLY HIS LEU TRP PHE ASP PHE TYR ARG ASN SEQRES 17 B 348 LEU PHE LEU LEU LYS GLY SER ASP ALA PHE LEU GLU ALA SEQRES 18 B 348 GLY LYS PRO GLY CYS HIS HIS LEU GLN PRO GLY GLY GLY SEQRES 19 B 348 CYS ILE TYR LEU ASP ALA ASP MET LEU LEU THR ASP LYS SEQRES 20 B 348 LEU GLY THR LEU TYR LEU PRO ASP GLY ILE ALA ILE HIS SEQRES 21 B 348 VAL SER ARG LYS ASP ASN HIS VAL SER LEU GLU ASN GLY SEQRES 22 B 348 ILE ILE ALA VAL ASN ARG SER GLU HIS PRO ALA LEU ILE SEQRES 23 B 348 LYS GLY LEU GLU ILE MET HIS SER LYS PRO TYR GLY ASP SEQRES 24 B 348 PRO TYR ASN ASP TRP LEU SER LYS GLY LEU ARG HIS TYR SEQRES 25 B 348 PHE ASP GLY SER HIS ILE GLN ASP TYR ASP ALA PHE CYS SEQRES 26 B 348 ASP PHE ILE GLU PHE LYS HIS GLU ASN ILE ILE MET ASN SEQRES 27 B 348 THR SER SER LEU THR ALA SER SER TRP ARG HET EDO A 401 4 HET EDO A 402 4 HET MN A 403 1 HET UDP A 404 25 HET MN A 405 1 HET EDO B 401 4 HET UDP B 402 25 HET MN B 403 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 3(C2 H6 O2) FORMUL 5 MN 3(MN 2+) FORMUL 6 UDP 2(C9 H14 N2 O12 P2) FORMUL 11 HOH *557(H2 O) HELIX 1 AA1 ASN A 69 PHE A 73 5 5 HELIX 2 AA2 PRO A 87 GLU A 99 1 13 HELIX 3 AA3 SER A 113 TYR A 127 1 15 HELIX 4 AA4 SER A 136 LEU A 138 5 3 HELIX 5 AA5 TYR A 140 ASP A 144 5 5 HELIX 6 AA6 LYS A 146 GLN A 161 1 16 HELIX 7 AA7 ASP A 167 ASN A 185 1 19 HELIX 8 AA8 THR A 189 HIS A 194 1 6 HELIX 9 AA9 ASN A 195 LYS A 198 5 4 HELIX 10 AB1 GLY A 199 GLY A 214 1 16 HELIX 11 AB2 SER A 215 ALA A 221 1 7 HELIX 12 AB3 HIS A 282 LYS A 295 1 14 HELIX 13 AB4 LEU A 305 ASP A 314 1 10 HELIX 14 AB5 ASP A 320 GLU A 329 1 10 HELIX 15 AB6 ASN A 338 THR A 343 5 6 HELIX 16 AB7 ASN B 69 PHE B 73 5 5 HELIX 17 AB8 PRO B 87 GLU B 99 1 13 HELIX 18 AB9 SER B 113 TYR B 127 1 15 HELIX 19 AC1 SER B 136 LEU B 138 5 3 HELIX 20 AC2 TYR B 140 ASP B 144 5 5 HELIX 21 AC3 LYS B 146 GLN B 161 1 16 HELIX 22 AC4 ASP B 167 ASN B 185 1 19 HELIX 23 AC5 ILE B 191 ASN B 195 5 5 HELIX 24 AC6 GLY B 199 GLY B 214 1 16 HELIX 25 AC7 SER B 215 ALA B 221 1 7 HELIX 26 AC8 HIS B 282 LYS B 295 1 14 HELIX 27 AC9 TRP B 304 ASP B 314 1 11 HELIX 28 AD1 ASP B 320 GLU B 329 1 10 SHEET 1 AA1 3 HIS A 42 PHE A 45 0 SHEET 2 AA1 3 ILE A 48 LEU A 55 -1 O TYR A 50 N VAL A 43 SHEET 3 AA1 3 LEU A 251 PRO A 254 -1 O LEU A 251 N LEU A 55 SHEET 1 AA2 6 ILE A 130 TYR A 134 0 SHEET 2 AA2 6 ILE A 104 ASP A 109 1 N VAL A 108 O ILE A 133 SHEET 3 AA2 6 LEU A 61 PHE A 66 1 N PHE A 63 O PHE A 107 SHEET 4 AA2 6 GLY A 233 LEU A 238 1 O LEU A 238 N VAL A 62 SHEET 5 AA2 6 SER A 269 ARG A 279 -1 O ILE A 275 N TYR A 237 SHEET 6 AA2 6 ILE A 257 SER A 262 -1 N ALA A 258 O ALA A 276 SHEET 1 AA3 2 LEU A 243 LEU A 244 0 SHEET 2 AA3 2 ILE A 335 ILE A 336 -1 O ILE A 336 N LEU A 243 SHEET 1 AA4 3 HIS B 42 PHE B 45 0 SHEET 2 AA4 3 ILE B 48 LEU B 55 -1 O TYR B 50 N VAL B 43 SHEET 3 AA4 3 LEU B 251 PRO B 254 -1 O LEU B 253 N LEU B 53 SHEET 1 AA5 6 ILE B 130 TYR B 134 0 SHEET 2 AA5 6 ILE B 104 ASP B 109 1 N ILE B 104 O LYS B 131 SHEET 3 AA5 6 LEU B 61 PHE B 66 1 N LEU B 61 O GLY B 105 SHEET 4 AA5 6 GLY B 233 LEU B 238 1 O ILE B 236 N VAL B 62 SHEET 5 AA5 6 VAL B 268 ARG B 279 -1 O ILE B 275 N TYR B 237 SHEET 6 AA5 6 ILE B 257 ARG B 263 -1 N HIS B 260 O GLU B 271 SHEET 1 AA6 2 LEU B 243 LEU B 244 0 SHEET 2 AA6 2 ILE B 335 ILE B 336 -1 O ILE B 336 N LEU B 243 LINK OD2 ASP A 241 MN MN A 403 1555 1555 2.23 LINK OD1 ASP A 322 MN MN A 405 1555 1555 2.27 LINK OD1 ASN A 338 MN MN A 403 1555 1555 2.20 LINK OG SER A 340 MN MN A 403 1555 1555 2.30 LINK MN MN A 403 O2B UDP A 404 1555 1555 2.10 LINK MN MN A 403 O1A UDP A 404 1555 1555 2.18 LINK MN MN A 403 O HOH A 572 1555 1555 2.11 LINK MN MN A 405 NE2 HIS B 267 1555 1555 2.27 LINK MN MN A 405 OG SER B 269 1555 1555 2.34 LINK MN MN A 405 O HOH B 566 1555 1555 2.14 LINK OD2 ASP B 241 MN MN B 403 1555 1555 2.26 LINK OG SER B 340 MN MN B 403 1555 1555 2.36 LINK O1A UDP B 402 MN MN B 403 1555 1555 2.11 LINK O1B UDP B 402 MN MN B 403 1555 1555 1.84 LINK MN MN B 403 O HOH B 511 1555 1555 2.07 LINK MN MN B 403 O HOH B 540 1555 1555 2.20 SITE 1 AC1 6 ASP A 239 GLU A 271 ASN A 272 GLY A 273 SITE 2 AC1 6 ARG A 348 UDP A 404 SITE 1 AC2 4 ASP A 109 ASN A 135 TRP A 202 TYR A 206 SITE 1 AC3 5 ASP A 241 ASN A 338 SER A 340 UDP A 404 SITE 2 AC3 5 HOH A 572 SITE 1 AC4 26 GLN A 64 TRP A 65 PHE A 66 TYR A 88 SITE 2 AC4 26 PHE A 203 ARG A 207 TYR A 237 ASP A 239 SITE 3 AC4 26 ALA A 240 ASP A 241 ASN A 338 SER A 340 SITE 4 AC4 26 SER A 345 SER A 346 TRP A 347 ARG A 348 SITE 5 AC4 26 EDO A 401 MN A 403 HOH A 507 HOH A 519 SITE 6 AC4 26 HOH A 568 HOH A 572 HOH A 580 HOH A 609 SITE 7 AC4 26 HOH A 611 HOH A 657 SITE 1 AC5 4 ASP A 322 HIS B 267 SER B 269 HOH B 566 SITE 1 AC6 6 HIS B 200 ASP B 204 ARG B 207 ASP B 239 SITE 2 AC6 6 ASN B 272 HOH B 536 SITE 1 AC7 23 SER A 164 GLU A 165 HOH A 508 GLN B 64 SITE 2 AC7 23 TRP B 65 PHE B 66 TYR B 88 HIS B 200 SITE 3 AC7 23 PHE B 203 ARG B 207 TYR B 237 ASP B 239 SITE 4 AC7 23 ALA B 240 ASP B 241 SER B 340 MN B 403 SITE 5 AC7 23 HOH B 511 HOH B 515 HOH B 532 HOH B 540 SITE 6 AC7 23 HOH B 587 HOH B 606 HOH B 641 SITE 1 AC8 5 ASP B 241 SER B 340 UDP B 402 HOH B 511 SITE 2 AC8 5 HOH B 540 CRYST1 49.590 143.630 52.730 90.00 108.24 90.00 P 1 21 1 4 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 0.020165 0.000000 0.006646 0.00000 SCALE2 0.000000 0.006962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019968 0.00000