HEADER OXIDOREDUCTASE 26-DEC-19 6TTB TITLE CRYSTAL STRUCTURE OF NAD-DEPENDENT FORMATE DEHYDROGENASE FROM TITLE 2 STAPHYLOCOCCUS AUREUS IN COMPLEX WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: M1K003_0593; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FORMATE DEHYDROGENASE, NAD, FORMATE OXIDATION, STAPHYLOCOCCUS AUREUS, KEYWDS 2 OXIDOREDUCTASE, COFACTOR EXPDTA X-RAY DIFFRACTION AUTHOR K.M.BOYKO,A.A.POMETUN,A.Y.NIKOLAEVA,I.S.KARGOV,T.S.YURCHENKO, AUTHOR 2 S.S.SAVIN,V.O.POPOV,V.I.TISHKOV REVDAT 2 24-JAN-24 6TTB 1 REMARK REVDAT 1 13-JAN-21 6TTB 0 JRNL AUTH K.M.BOYKO,A.A.POMETUN,A.Y.NIKOLAEVA,I.S.KARGOV, JRNL AUTH 2 T.S.YURCHENKO,S.S.SAVIN,V.I.TISHKOV JRNL TITL CRYSTAL STRUCTURE OF NAD-DEPENDENT FORMATE DEHYDROGENASE JRNL TITL 2 FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH NAD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18930 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1021 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1390 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5040 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.10000 REMARK 3 B22 (A**2) : 21.39000 REMARK 3 B33 (A**2) : -23.50000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.599 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5202 ; 0.017 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7094 ; 1.823 ; 1.628 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 9.811 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 269 ;36.888 ;22.788 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 792 ;23.473 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.973 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 700 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4031 ; 0.016 ; 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): 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 33 363 B 33 363 9268 0.190 0.050 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6TTB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-15 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 87.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.21500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 3N7U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HEPES PH7.5, 1.4M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 10% TREHALOSE, 7MM NAD, 10 MM AZIDE., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.64500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.68000 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: 6850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 SER A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 VAL A 5 REMARK 465 PHE A 6 REMARK 465 PHE A 7 REMARK 465 VAL A 8 REMARK 465 ILE A 9 REMARK 465 PHE A 10 REMARK 465 LEU A 11 REMARK 465 LYS A 12 REMARK 465 GLN A 13 REMARK 465 ALA A 14 REMARK 465 THR A 15 REMARK 465 CYS A 16 REMARK 465 ASN A 17 REMARK 465 THR A 18 REMARK 465 TYR A 19 REMARK 465 PHE A 20 REMARK 465 LYS A 21 REMARK 465 GLU A 22 REMARK 465 VAL A 23 REMARK 465 LYS A 24 REMARK 465 ILE A 25 REMARK 465 TYR A 26 REMARK 465 HIS A 27 REMARK 465 LEU A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 MET A 31 REMARK 465 ASP A 32 REMARK 465 ARG A 364 REMARK 465 ILE A 365 REMARK 465 ALA A 366 REMARK 465 SER A 367 REMARK 465 LYS A 368 REMARK 465 SER A 369 REMARK 465 TYR A 370 REMARK 465 THR A 371 REMARK 465 ALA A 372 REMARK 465 LYS A 373 REMARK 465 SER B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 3 REMARK 465 ALA B 4 REMARK 465 VAL B 5 REMARK 465 PHE B 6 REMARK 465 PHE B 7 REMARK 465 VAL B 8 REMARK 465 ILE B 9 REMARK 465 PHE B 10 REMARK 465 LEU B 11 REMARK 465 LYS B 12 REMARK 465 GLN B 13 REMARK 465 ALA B 14 REMARK 465 THR B 15 REMARK 465 CYS B 16 REMARK 465 ASN B 17 REMARK 465 THR B 18 REMARK 465 TYR B 19 REMARK 465 PHE B 20 REMARK 465 LYS B 21 REMARK 465 GLU B 22 REMARK 465 VAL B 23 REMARK 465 LYS B 24 REMARK 465 ILE B 25 REMARK 465 TYR B 26 REMARK 465 HIS B 27 REMARK 465 LEU B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 465 MET B 31 REMARK 465 ASP B 32 REMARK 465 GLU B 44 REMARK 465 GLY B 45 REMARK 465 GLN B 46 REMARK 465 ALA B 74 REMARK 465 ASP B 75 REMARK 465 ASN B 76 REMARK 465 ALA B 366 REMARK 465 SER B 367 REMARK 465 LYS B 368 REMARK 465 SER B 369 REMARK 465 TYR B 370 REMARK 465 THR B 371 REMARK 465 ALA B 372 REMARK 465 LYS B 373 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 GLU A 44 CG CD OE1 OE2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 55 CD CE NZ REMARK 470 ILE A 72 CD1 REMARK 470 ASP A 75 CG OD1 OD2 REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 ASP A 81 CG OD1 OD2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 223 CG CD OE1 NE2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 ASP A 234 CG OD1 OD2 REMARK 470 SER A 263 OG REMARK 470 LYS A 267 CG CD CE NZ REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 LYS A 334 CG CD CE NZ REMARK 470 GLN A 354 CG CD OE1 NE2 REMARK 470 ASP A 355 CG OD1 OD2 REMARK 470 LYS A 356 CE NZ REMARK 470 GLU B 41 CG CD OE1 OE2 REMARK 470 VAL B 43 CG1 CG2 REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 LYS B 55 CE NZ REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 ILE B 72 CD1 REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 ASP B 79 CG OD1 OD2 REMARK 470 LEU B 80 CG CD1 CD2 REMARK 470 LYS B 82 CG CD CE NZ REMARK 470 GLU B 103 CG CD OE1 OE2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 ILE B 193 CD1 REMARK 470 GLN B 223 CG CD OE1 NE2 REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 SER B 228 OG REMARK 470 LYS B 229 CG CD CE NZ REMARK 470 LYS B 259 NZ REMARK 470 LYS B 267 CE NZ REMARK 470 LYS B 278 CG CD CE NZ REMARK 470 GLU B 287 CG CD OE1 OE2 REMARK 470 SER B 326 OG REMARK 470 LYS B 334 CG CD CE NZ REMARK 470 GLU B 345 CD OE1 OE2 REMARK 470 SER B 362 OG 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 GLU A 106 CD GLU A 106 OE2 0.082 REMARK 500 SER A 121 CA SER A 121 CB -0.091 REMARK 500 GLU B 149 CD GLU B 149 OE1 0.078 REMARK 500 GLU B 351 CD GLU B 351 OE1 0.068 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 ASN B 161 CB - CA - C ANGL. DEV. = 16.3 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 GLN A 46 66.92 -69.66 REMARK 500 ALA A 56 47.04 30.94 REMARK 500 ILE A 57 29.56 47.41 REMARK 500 GLU A 64 1.86 -64.63 REMARK 500 ASP A 75 -55.62 -149.33 REMARK 500 ASN A 76 -79.64 79.90 REMARK 500 GLU A 78 -46.04 94.52 REMARK 500 ASP A 86 -12.37 -146.52 REMARK 500 TYR A 96 71.15 -167.31 REMARK 500 MET A 100 78.79 -105.66 REMARK 500 ALA A 108 76.44 -114.10 REMARK 500 PRO A 109 0.19 -69.36 REMARK 500 ALA A 117 82.53 -66.97 REMARK 500 ASP A 125 91.80 -69.59 REMARK 500 ASN A 143 24.94 -151.33 REMARK 500 TRP A 174 90.99 -166.15 REMARK 500 HIS A 188 -1.11 77.30 REMARK 500 PHE A 196 53.32 -111.68 REMARK 500 ASN A 211 83.07 73.68 REMARK 500 ALA A 275 -84.14 -94.98 REMARK 500 GLU A 292 15.27 80.98 REMARK 500 PRO A 317 132.94 -27.15 REMARK 500 THR A 329 154.15 -46.17 REMARK 500 LYS A 356 -46.26 -22.17 REMARK 500 ALA B 42 -169.11 -70.28 REMARK 500 ASN B 48 29.45 -74.55 REMARK 500 ILE B 57 28.36 47.30 REMARK 500 GLU B 64 0.89 -67.79 REMARK 500 LEU B 80 58.21 -94.91 REMARK 500 LYS B 82 44.56 -62.48 REMARK 500 HIS B 83 -14.63 -172.91 REMARK 500 ASP B 86 -11.62 -161.88 REMARK 500 TYR B 96 67.42 -165.78 REMARK 500 ALA B 108 60.09 -118.71 REMARK 500 THR B 140 47.94 -79.05 REMARK 500 ASN B 161 52.37 -97.75 REMARK 500 TRP B 174 68.82 -156.36 REMARK 500 ASN B 175 -96.83 -65.98 REMARK 500 LEU B 176 -43.00 112.93 REMARK 500 HIS B 188 -6.96 80.10 REMARK 500 PHE B 196 55.42 -107.78 REMARK 500 LEU B 227 -67.12 143.00 REMARK 500 ALA B 275 -85.86 -93.97 REMARK 500 SER B 326 -44.82 149.65 REMARK 500 SER B 362 100.15 -175.47 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 LEU A 73 ALA A 74 134.94 REMARK 500 LEU B 51 ASN B 52 -149.04 REMARK 500 LEU B 80 ASP B 81 132.03 REMARK 500 PRO B 97 ALA B 98 149.98 REMARK 500 SER B 326 GLY B 327 144.94 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 NAD A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E0D RELATED DB: PDB REMARK 900 APO ENZYME DBREF1 6TTB A 1 373 UNP A0A389UHR2_STAAU DBREF2 6TTB A A0A389UHR2 19 391 DBREF1 6TTB B 1 373 UNP A0A389UHR2_STAAU DBREF2 6TTB B A0A389UHR2 19 391 SEQRES 1 A 373 SER ASN GLY ALA VAL PHE PHE VAL ILE PHE LEU LYS GLN SEQRES 2 A 373 ALA THR CYS ASN THR TYR PHE LYS GLU VAL LYS ILE TYR SEQRES 3 A 373 HIS LEU GLY GLU MET ASP MET LYS ILE VAL ALA LEU PHE SEQRES 4 A 373 PRO GLU ALA VAL GLU GLY GLN GLU ASN GLN LEU LEU ASN SEQRES 5 A 373 THR LYS LYS ALA ILE GLY LEU LYS THR PHE LEU GLU GLU SEQRES 6 A 373 ARG GLY HIS GLU PHE ILE ILE LEU ALA ASP ASN GLY GLU SEQRES 7 A 373 ASP LEU ASP LYS HIS LEU PRO ASP MET ASP VAL ILE ILE SEQRES 8 A 373 SER ALA PRO PHE TYR PRO ALA TYR MET THR ARG GLU ARG SEQRES 9 A 373 ILE GLU LYS ALA PRO ASN LEU LYS LEU ALA ILE THR ALA SEQRES 10 A 373 GLY VAL GLY SER ASP HIS VAL ASP LEU ALA ALA ALA SER SEQRES 11 A 373 GLU HIS ASN ILE GLY VAL VAL GLU VAL THR GLY SER ASN SEQRES 12 A 373 THR VAL SER VAL ALA GLU HIS ALA VAL MET ASP LEU LEU SEQRES 13 A 373 ILE LEU LEU ARG ASN TYR GLU GLU GLY HIS ARG GLN SER SEQRES 14 A 373 VAL GLU GLY GLU TRP ASN LEU SER GLN VAL GLY ASN HIS SEQRES 15 A 373 ALA HIS GLU LEU GLN HIS LYS THR ILE GLY ILE PHE GLY SEQRES 16 A 373 PHE GLY ARG ILE GLY GLN LEU VAL ALA GLU ARG LEU ALA SEQRES 17 A 373 PRO PHE ASN VAL THR LEU GLN HIS TYR ASP PRO ILE ASN SEQRES 18 A 373 GLN GLN ASP HIS LYS LEU SER LYS PHE VAL SER PHE ASP SEQRES 19 A 373 GLU LEU VAL SER SER SER ASP ALA ILE THR ILE HIS ALA SEQRES 20 A 373 PRO LEU THR PRO GLU THR ASP ASN LEU PHE ASP LYS ASP SEQRES 21 A 373 VAL LEU SER ARG MET LYS LYS HIS SER TYR LEU VAL ASN SEQRES 22 A 373 THR ALA ARG GLY LYS ILE VAL ASN ARG ASP ALA LEU VAL SEQRES 23 A 373 GLU ALA LEU ALA SER GLU HIS LEU GLN GLY TYR ALA GLY SEQRES 24 A 373 ASP VAL TRP TYR PRO GLN PRO ALA PRO ALA ASP HIS PRO SEQRES 25 A 373 TRP ARG THR MET PRO ARG ASN ALA MET THR VAL HIS TYR SEQRES 26 A 373 SER GLY MET THR LEU GLU ALA GLN LYS ARG ILE GLU ASP SEQRES 27 A 373 GLY VAL LYS ASP ILE LEU GLU ARG PHE PHE ASN HIS GLU SEQRES 28 A 373 PRO PHE GLN ASP LYS ASP ILE ILE VAL ALA SER GLY ARG SEQRES 29 A 373 ILE ALA SER LYS SER TYR THR ALA LYS SEQRES 1 B 373 SER ASN GLY ALA VAL PHE PHE VAL ILE PHE LEU LYS GLN SEQRES 2 B 373 ALA THR CYS ASN THR TYR PHE LYS GLU VAL LYS ILE TYR SEQRES 3 B 373 HIS LEU GLY GLU MET ASP MET LYS ILE VAL ALA LEU PHE SEQRES 4 B 373 PRO GLU ALA VAL GLU GLY GLN GLU ASN GLN LEU LEU ASN SEQRES 5 B 373 THR LYS LYS ALA ILE GLY LEU LYS THR PHE LEU GLU GLU SEQRES 6 B 373 ARG GLY HIS GLU PHE ILE ILE LEU ALA ASP ASN GLY GLU SEQRES 7 B 373 ASP LEU ASP LYS HIS LEU PRO ASP MET ASP VAL ILE ILE SEQRES 8 B 373 SER ALA PRO PHE TYR PRO ALA TYR MET THR ARG GLU ARG SEQRES 9 B 373 ILE GLU LYS ALA PRO ASN LEU LYS LEU ALA ILE THR ALA SEQRES 10 B 373 GLY VAL GLY SER ASP HIS VAL ASP LEU ALA ALA ALA SER SEQRES 11 B 373 GLU HIS ASN ILE GLY VAL VAL GLU VAL THR GLY SER ASN SEQRES 12 B 373 THR VAL SER VAL ALA GLU HIS ALA VAL MET ASP LEU LEU SEQRES 13 B 373 ILE LEU LEU ARG ASN TYR GLU GLU GLY HIS ARG GLN SER SEQRES 14 B 373 VAL GLU GLY GLU TRP ASN LEU SER GLN VAL GLY ASN HIS SEQRES 15 B 373 ALA HIS GLU LEU GLN HIS LYS THR ILE GLY ILE PHE GLY SEQRES 16 B 373 PHE GLY ARG ILE GLY GLN LEU VAL ALA GLU ARG LEU ALA SEQRES 17 B 373 PRO PHE ASN VAL THR LEU GLN HIS TYR ASP PRO ILE ASN SEQRES 18 B 373 GLN GLN ASP HIS LYS LEU SER LYS PHE VAL SER PHE ASP SEQRES 19 B 373 GLU LEU VAL SER SER SER ASP ALA ILE THR ILE HIS ALA SEQRES 20 B 373 PRO LEU THR PRO GLU THR ASP ASN LEU PHE ASP LYS ASP SEQRES 21 B 373 VAL LEU SER ARG MET LYS LYS HIS SER TYR LEU VAL ASN SEQRES 22 B 373 THR ALA ARG GLY LYS ILE VAL ASN ARG ASP ALA LEU VAL SEQRES 23 B 373 GLU ALA LEU ALA SER GLU HIS LEU GLN GLY TYR ALA GLY SEQRES 24 B 373 ASP VAL TRP TYR PRO GLN PRO ALA PRO ALA ASP HIS PRO SEQRES 25 B 373 TRP ARG THR MET PRO ARG ASN ALA MET THR VAL HIS TYR SEQRES 26 B 373 SER GLY MET THR LEU GLU ALA GLN LYS ARG ILE GLU ASP SEQRES 27 B 373 GLY VAL LYS ASP ILE LEU GLU ARG PHE PHE ASN HIS GLU SEQRES 28 B 373 PRO PHE GLN ASP LYS ASP ILE ILE VAL ALA SER GLY ARG SEQRES 29 B 373 ILE ALA SER LYS SER TYR THR ALA LYS HET NAD A 401 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 HOH *12(H2 O) HELIX 1 AA1 LYS A 55 ILE A 57 5 3 HELIX 2 AA2 GLY A 58 GLU A 65 1 8 HELIX 3 AA3 THR A 101 LYS A 107 1 7 HELIX 4 AA4 ASP A 125 HIS A 132 1 8 HELIX 5 AA5 ASN A 143 ASN A 161 1 19 HELIX 6 AA6 ASN A 161 GLY A 172 1 12 HELIX 7 AA7 ASN A 175 ASN A 181 1 7 HELIX 8 AA8 GLY A 197 ALA A 208 1 12 HELIX 9 AA9 PRO A 209 ASN A 211 5 3 HELIX 10 AB1 SER A 232 SER A 240 1 9 HELIX 11 AB2 ASP A 258 MET A 265 1 8 HELIX 12 AB3 ARG A 276 VAL A 280 5 5 HELIX 13 AB4 ASN A 281 SER A 291 1 11 HELIX 14 AB5 TYR A 325 MET A 328 5 4 HELIX 15 AB6 THR A 329 ASN A 349 1 21 HELIX 16 AB7 GLN A 354 LYS A 356 5 3 HELIX 17 AB8 LYS B 55 ILE B 57 5 3 HELIX 18 AB9 GLY B 58 GLU B 65 1 8 HELIX 19 AC1 THR B 101 LYS B 107 1 7 HELIX 20 AC2 ASP B 125 HIS B 132 1 8 HELIX 21 AC3 ASN B 143 ARG B 160 1 18 HELIX 22 AC4 ASN B 161 GLY B 172 1 12 HELIX 23 AC5 LEU B 176 ASN B 181 1 6 HELIX 24 AC6 GLY B 197 ALA B 208 1 12 HELIX 25 AC7 PRO B 209 ASN B 211 5 3 HELIX 26 AC8 SER B 232 SER B 240 1 9 HELIX 27 AC9 ASP B 258 MET B 265 1 8 HELIX 28 AD1 ARG B 276 VAL B 280 5 5 HELIX 29 AD2 ASN B 281 SER B 291 1 11 HELIX 30 AD3 HIS B 311 MET B 316 1 6 HELIX 31 AD4 THR B 329 ASN B 349 1 21 HELIX 32 AD5 GLN B 354 LYS B 356 5 3 SHEET 1 AA1 6 GLU A 69 LEU A 73 0 SHEET 2 AA1 6 LYS A 34 LEU A 38 1 N ALA A 37 O ILE A 71 SHEET 3 AA1 6 VAL A 89 SER A 92 1 O VAL A 89 N VAL A 36 SHEET 4 AA1 6 LEU A 113 THR A 116 1 O ILE A 115 N ILE A 90 SHEET 5 AA1 6 GLY A 135 GLU A 138 1 O GLY A 135 N ALA A 114 SHEET 6 AA1 6 ILE A 358 VAL A 360 -1 O ILE A 359 N VAL A 136 SHEET 1 AA2 7 LYS A 229 PHE A 230 0 SHEET 2 AA2 7 THR A 213 TYR A 217 1 N LEU A 214 O LYS A 229 SHEET 3 AA2 7 THR A 190 PHE A 194 1 N ILE A 191 O THR A 213 SHEET 4 AA2 7 ALA A 242 ILE A 245 1 O THR A 244 N PHE A 194 SHEET 5 AA2 7 SER A 269 ASN A 273 1 O VAL A 272 N ILE A 243 SHEET 6 AA2 7 LEU A 294 GLY A 299 1 O GLN A 295 N SER A 269 SHEET 7 AA2 7 ASN A 319 MET A 321 1 O ALA A 320 N TYR A 297 SHEET 1 AA3 6 GLU B 69 LEU B 73 0 SHEET 2 AA3 6 LYS B 34 LEU B 38 1 N ILE B 35 O GLU B 69 SHEET 3 AA3 6 VAL B 89 SER B 92 1 O VAL B 89 N VAL B 36 SHEET 4 AA3 6 LEU B 113 THR B 116 1 O ILE B 115 N ILE B 90 SHEET 5 AA3 6 GLY B 135 GLU B 138 1 O GLY B 135 N ALA B 114 SHEET 6 AA3 6 ILE B 358 VAL B 360 -1 O ILE B 359 N VAL B 136 SHEET 1 AA4 7 SER B 228 PHE B 230 0 SHEET 2 AA4 7 THR B 213 TYR B 217 1 N LEU B 214 O LYS B 229 SHEET 3 AA4 7 THR B 190 PHE B 194 1 N ILE B 191 O THR B 213 SHEET 4 AA4 7 ALA B 242 ILE B 245 1 O THR B 244 N GLY B 192 SHEET 5 AA4 7 SER B 269 ASN B 273 1 O VAL B 272 N ILE B 243 SHEET 6 AA4 7 LEU B 294 GLY B 299 1 O GLN B 295 N SER B 269 SHEET 7 AA4 7 ASN B 319 MET B 321 1 O ALA B 320 N TYR B 297 CISPEP 1 TYR A 303 PRO A 304 0 -6.13 CISPEP 2 GLN A 305 PRO A 306 0 0.31 CISPEP 3 TYR B 303 PRO B 304 0 -3.42 CISPEP 4 GLN B 305 PRO B 306 0 -7.20 SITE 1 AC1 23 PHE A 95 ASN A 143 VAL A 147 PHE A 194 SITE 2 AC1 23 GLY A 197 ARG A 198 ILE A 199 TYR A 217 SITE 3 AC1 23 ASP A 218 PRO A 219 HIS A 246 ALA A 247 SITE 4 AC1 23 PRO A 248 GLU A 252 THR A 253 THR A 274 SITE 5 AC1 23 ARG A 276 ASP A 300 HIS A 324 SER A 326 SITE 6 AC1 23 GLY A 327 HOH A 502 HOH A 504 CRYST1 69.290 87.360 117.630 90.00 90.00 90.00 P 21 21 21 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 0.014432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008501 0.00000