HEADER BIOSYNTHETIC PROTEIN 18-JUL-18 6H3D TITLE STAPHYLOPINE DEHYDROGENASE IN COMPLEX WITH XNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF2338 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: RK60_12795, RK98_07680, RL06_05590, SAMEA3448991_00758; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS STAPHYLOPINE BIOSYNTHESIS, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.HAJJAR,P.ARNOUX REVDAT 2 17-JAN-24 6H3D 1 REMARK REVDAT 1 10-APR-19 6H3D 0 JRNL AUTH C.HAJJAR,R.FANELLI,C.LAFFONT,C.BRUTESCO,G.CULLIA,M.TRIBOUT, JRNL AUTH 2 D.NURIZZO,E.BOREZEE-DURANT,R.VOULHOUX,D.PIGNOL,J.LAVERGNE, JRNL AUTH 3 F.CAVELIER,P.ARNOUX JRNL TITL CONTROL BY METALS OF STAPHYLOPINE DEHYDROGENASE ACTIVITY JRNL TITL 2 DURING METALLOPHORE BIOSYNTHESIS. JRNL REF J.AM.CHEM.SOC. V. 141 5555 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 30901200 JRNL DOI 10.1021/JACS.9B01676 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 92.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 32581 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1733 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2368 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.4260 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.73000 REMARK 3 B22 (A**2) : -2.86000 REMARK 3 B33 (A**2) : 3.59000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.966 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3692 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3385 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5001 ; 2.225 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7899 ; 1.152 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 7.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;38.187 ;24.911 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 661 ;18.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 554 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3945 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 724 ; 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): 1716 ; 5.018 ; 4.964 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1715 ; 5.010 ; 4.961 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2142 ; 6.315 ; 7.441 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2143 ; 6.318 ; 7.444 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 6.920 ; 5.921 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1976 ; 6.919 ; 5.922 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2859 ;10.065 ; 8.589 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4125 ;12.014 ;59.886 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4112 ;12.016 ;59.836 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 : NULL 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 6H3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-17 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 142598 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 92.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6GMZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 22% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 92.54500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 92.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.37500 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: 7240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 48.75000 REMARK 350 BIOMT3 2 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 ARG A 430 REMARK 465 THR A 431 REMARK 465 LEU A 432 REMARK 465 SER A 433 REMARK 465 LEU A 434 REMARK 465 GLU A 435 REMARK 465 HIS A 436 REMARK 465 HIS A 437 REMARK 465 HIS A 438 REMARK 465 HIS A 439 REMARK 465 HIS A 440 REMARK 465 HIS A 441 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 SD MET A 256 O HOH A 823 2.14 REMARK 500 OE1 GLU A 60 NE2 GLN A 63 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 338 CB SER A 338 OG -0.101 REMARK 500 GLU A 361 CD GLU A 361 OE2 0.070 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 LEU A 43 CA - CB - CG ANGL. DEV. = -17.0 DEGREES REMARK 500 GLN A 52 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 CYS A 92 CA - CB - SG ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 223 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 MET A 263 CG - SD - CE ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 289 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 316 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 316 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 389 NE - CZ - NH2 ANGL. DEV. = -3.2 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 SER A 35 -59.68 -25.51 REMARK 500 SER A 37 120.77 -170.53 REMARK 500 HIS A 64 -36.10 -20.26 REMARK 500 ALA A 158 65.12 -117.34 REMARK 500 ASN A 179 26.94 49.38 REMARK 500 ARG A 209 47.88 -92.50 REMARK 500 MET A 221 54.46 -112.77 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 THR A 412 ASN A 413 -46.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DHI A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 603 DBREF1 6H3D A 1 433 UNP A0A1K7Y513_STAAU DBREF2 6H3D A A0A1K7Y513 1 433 SEQADV 6H3D LEU A 434 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D GLU A 435 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 436 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 437 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 438 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 439 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 440 UNP A0A1K7Y51 EXPRESSION TAG SEQADV 6H3D HIS A 441 UNP A0A1K7Y51 EXPRESSION TAG SEQRES 1 A 441 MET SER LYS LEU LEU MET ILE GLY THR GLY PRO VAL ALA SEQRES 2 A 441 ILE GLN LEU ALA ASN ILE CYS TYR LEU LYS SER ASP TYR SEQRES 3 A 441 GLU ILE ASP MET VAL GLY ARG ALA SER THR SER GLU LYS SEQRES 4 A 441 SER LYS ARG LEU TYR GLN ALA TYR LYS LYS GLU LYS GLN SEQRES 5 A 441 PHE GLU VAL LYS ILE GLN ASN GLU ALA HIS GLN HIS LEU SEQRES 6 A 441 GLU GLY LYS PHE GLU ILE ASN ARG LEU TYR LYS ASP VAL SEQRES 7 A 441 LYS ASN VAL LYS GLY GLU TYR GLU THR VAL VAL MET ALA SEQRES 8 A 441 CYS THR ALA ASP ALA TYR TYR ASP THR LEU GLN GLN LEU SEQRES 9 A 441 SER LEU GLU THR LEU GLN SER VAL LYS HIS VAL ILE LEU SEQRES 10 A 441 ILE SER PRO THR PHE GLY SER GLN MET ILE VAL GLU GLN SEQRES 11 A 441 PHE MET SER LYS PHE SER GLN ASP ILE GLU VAL ILE SER SEQRES 12 A 441 PHE SER THR TYR LEU GLY ASP THR ARG ILE VAL ASP LYS SEQRES 13 A 441 GLU ALA PRO ASN HIS VAL LEU THR THR GLY VAL LYS LYS SEQRES 14 A 441 LYS LEU TYR MET GLY SER THR HIS SER ASN SER THR MET SEQRES 15 A 441 CYS GLN ARG ILE SER ALA LEU ALA GLU GLN LEU LYS ILE SEQRES 16 A 441 GLN LEU GLU VAL VAL GLU SER PRO LEU HIS ALA GLU THR SEQRES 17 A 441 ARG ASN SER SER LEU TYR VAL HIS PRO PRO LEU PHE MET SEQRES 18 A 441 ASN ASP PHE SER LEU LYS ALA ILE PHE GLU GLY THR ASP SEQRES 19 A 441 VAL PRO VAL TYR VAL TYR LYS LEU PHE PRO GLU GLY PRO SEQRES 20 A 441 ILE THR MET THR LEU ILE ARG GLU MET ARG LEU MET TRP SEQRES 21 A 441 LYS GLU MET MET ALA ILE LEU GLN ALA PHE ARG VAL PRO SEQRES 22 A 441 SER VAL ASN LEU LEU GLN PHE MET VAL LYS GLU ASN TYR SEQRES 23 A 441 PRO VAL ARG PRO GLU THR LEU ASP GLU GLY ASP ILE GLU SEQRES 24 A 441 HIS PHE GLU ILE LEU PRO ASP ILE LEU GLN GLU TYR LEU SEQRES 25 A 441 LEU TYR VAL ARG TYR THR ALA ILE LEU ILE ASP PRO PHE SEQRES 26 A 441 SER GLN PRO ASP GLU ASN GLY HIS TYR PHE ASP PHE SER SEQRES 27 A 441 ALA VAL PRO PHE LYS GLN VAL TYR LYS ASN GLU GLN ASP SEQRES 28 A 441 VAL VAL GLN ILE PRO ARG MET PRO SER GLU ASP TYR TYR SEQRES 29 A 441 ARG THR ALA MET ILE GLN HIS ILE GLY LYS MET LEU GLY SEQRES 30 A 441 ILE LYS THR PRO MET ILE ASP GLN PHE LEU THR ARG TYR SEQRES 31 A 441 GLU ALA SER CYS GLN ALA TYR LYS ASP MET HIS GLN ASP SEQRES 32 A 441 GLN GLN LEU SER SER GLN PHE ASN THR ASN LEU PHE GLU SEQRES 33 A 441 GLY ASP LYS ALA LEU VAL THR LYS PHE LEU GLU ILE ASN SEQRES 34 A 441 ARG THR LEU SER LEU GLU HIS HIS HIS HIS HIS HIS HET NDP A 600 96 HET DHI A 601 11 HET GOL A 602 6 HET PG4 A 603 13 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM DHI D-HISTIDINE HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 DHI C6 H10 N3 O2 1+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 PG4 C8 H18 O5 FORMUL 6 HOH *128(H2 O) HELIX 1 AA1 GLY A 10 SER A 24 1 15 HELIX 2 AA2 ARG A 33 THR A 36 5 4 HELIX 3 AA3 SER A 37 LYS A 51 1 15 HELIX 4 AA4 ASN A 59 GLU A 66 5 8 HELIX 5 AA5 ASP A 77 VAL A 81 5 5 HELIX 6 AA6 THR A 93 ASP A 95 5 3 HELIX 7 AA7 ALA A 96 GLN A 102 1 7 HELIX 8 AA8 SER A 105 VAL A 112 1 8 HELIX 9 AA9 GLY A 123 SER A 133 1 11 HELIX 10 AB1 SER A 180 LEU A 193 1 14 HELIX 11 AB2 SER A 202 THR A 208 1 7 HELIX 12 AB3 SER A 211 MET A 221 1 11 HELIX 13 AB4 ASN A 222 GLU A 231 1 10 HELIX 14 AB5 THR A 249 PHE A 270 1 22 HELIX 15 AB6 ASN A 276 GLU A 284 1 9 HELIX 16 AB7 ASP A 294 HIS A 300 1 7 HELIX 17 AB8 PHE A 301 LEU A 304 5 4 HELIX 18 AB9 PRO A 305 ILE A 320 1 16 HELIX 19 AC1 PRO A 356 LEU A 376 1 21 HELIX 20 AC2 THR A 380 HIS A 401 1 22 HELIX 21 AC3 SER A 408 ASN A 411 5 4 HELIX 22 AC4 PHE A 415 ASN A 429 1 15 SHEET 1 AA1 8 ARG A 73 TYR A 75 0 SHEET 2 AA1 8 GLU A 27 VAL A 31 1 N MET A 30 O TYR A 75 SHEET 3 AA1 8 LYS A 3 ILE A 7 1 N MET A 6 O ASP A 29 SHEET 4 AA1 8 THR A 87 MET A 90 1 O VAL A 89 N LEU A 5 SHEET 5 AA1 8 HIS A 114 LEU A 117 1 O ILE A 116 N MET A 90 SHEET 6 AA1 8 GLU A 140 PHE A 144 1 O ILE A 142 N LEU A 117 SHEET 7 AA1 8 LYS A 170 SER A 175 -1 O GLY A 174 N SER A 143 SHEET 8 AA1 8 GLN A 196 VAL A 200 1 O GLU A 198 N LEU A 171 SHEET 1 AA2 4 GLY A 67 PHE A 69 0 SHEET 2 AA2 4 PHE A 53 ILE A 57 -1 N PHE A 53 O PHE A 69 SHEET 3 AA2 4 HIS A 161 VAL A 167 1 O VAL A 162 N LYS A 56 SHEET 4 AA2 4 GLY A 149 ARG A 152 -1 N ARG A 152 O LEU A 163 SHEET 1 AA3 3 TYR A 346 LYS A 347 0 SHEET 2 AA3 3 VAL A 352 GLN A 354 -1 O GLN A 354 N TYR A 346 SHEET 3 AA3 3 GLN A 405 LEU A 406 1 O GLN A 405 N VAL A 353 CISPEP 1 PHE A 243 PRO A 244 0 14.74 CISPEP 2 MET A 358 PRO A 359 0 15.61 SITE 1 AC1 26 THR A 9 GLY A 10 PRO A 11 VAL A 12 SITE 2 AC1 26 ARG A 33 SER A 37 LYS A 39 SER A 40 SITE 3 AC1 26 ALA A 91 CYS A 92 THR A 93 ASP A 99 SITE 4 AC1 26 THR A 100 SER A 119 GLY A 149 ASP A 150 SITE 5 AC1 26 THR A 151 ARG A 357 HOH A 718 HOH A 732 SITE 6 AC1 26 HOH A 738 HOH A 739 HOH A 740 HOH A 750 SITE 7 AC1 26 HOH A 769 HOH A 776 SITE 1 AC2 6 TYR A 240 ASN A 285 ARG A 316 PHE A 337 SITE 2 AC2 6 HOH A 703 HOH A 747 SITE 1 AC3 9 ALA A 228 GLY A 232 THR A 233 PRO A 236 SITE 2 AC3 9 VAL A 237 PRO A 341 PHE A 342 GLN A 344 SITE 3 AC3 9 HOH A 758 SITE 1 AC4 1 ARG A 185 CRYST1 185.090 48.750 59.400 90.00 90.00 90.00 P 21 21 2 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 0.005403 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016835 0.00000