HEADER LYASE 19-JUN-08 3DI1 TITLE CRYSTAL STRUCTURE OF THE STAPHYLOCOCCUS AUREUS DIHYDRODIPICOLINATE TITLE 2 SYNTHASE-PYRUVATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHDPS; COMPND 5 EC: 4.2.1.52; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 93062; SOURCE 4 STRAIN: COL; SOURCE 5 GENE: DHDPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B-DHDPS KEYWDS DIHYDRODIPICOLINATE SYNTHASE, LYSINE BIOSYNTHESIS, FEEDBACK KEYWDS 2 INHIBITION, PING-PONG MECHANISM, AMINO-ACID BIOSYNTHESIS, KEYWDS 3 DIAMINOPIMELATE BIOSYNTHESIS, LYASE, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR G.S.TAVAREKERE REVDAT 7 30-OCT-24 3DI1 1 REMARK REVDAT 6 15-NOV-23 3DI1 1 LINK ATOM REVDAT 5 01-NOV-23 3DI1 1 REMARK LINK REVDAT 4 13-JUL-11 3DI1 1 VERSN REVDAT 3 24-FEB-09 3DI1 1 VERSN REVDAT 2 16-SEP-08 3DI1 1 JRNL REVDAT 1 12-AUG-08 3DI1 0 JRNL AUTH T.S.GIRISH,E.SHARMA,B.GOPAL JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF STAPHYLOCOCCUS JRNL TITL 2 AUREUS DIHYDRODIPICOLINATE SYNTHASE JRNL REF FEBS LETT. V. 582 2923 2008 JRNL REFN ISSN 0014-5793 JRNL PMID 18671976 JRNL DOI 10.1016/J.FEBSLET.2008.07.035 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 36520 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1923 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2637 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.42000 REMARK 3 B12 (A**2) : 0.14000 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): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.485 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4605 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6269 ; 1.536 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 6.294 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;36.834 ;25.842 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 792 ;14.236 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.509 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 759 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3424 ; 0.008 ; 0.021 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): 2899 ; 0.508 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4733 ; 1.005 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1706 ; 1.799 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1536 ; 2.960 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 291 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8790 -31.8493 -1.7866 REMARK 3 T TENSOR REMARK 3 T11: -0.1026 T22: -0.2147 REMARK 3 T33: -0.1086 T12: -0.0424 REMARK 3 T13: -0.0089 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.1907 L22: 2.2195 REMARK 3 L33: 2.3650 L12: 0.4356 REMARK 3 L13: -0.0942 L23: -0.6646 REMARK 3 S TENSOR REMARK 3 S11: -0.0199 S12: -0.0743 S13: -0.1179 REMARK 3 S21: -0.0595 S22: 0.0596 S23: 0.1070 REMARK 3 S31: 0.1712 S32: -0.1491 S33: -0.0396 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 291 REMARK 3 ORIGIN FOR THE GROUP (A): 45.1625 -13.9496 -28.3264 REMARK 3 T TENSOR REMARK 3 T11: -0.0426 T22: -0.1627 REMARK 3 T33: -0.1200 T12: -0.0132 REMARK 3 T13: 0.0206 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 1.2608 L22: 2.0496 REMARK 3 L33: 3.2255 L12: 0.4972 REMARK 3 L13: -0.0489 L23: -1.4957 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: 0.2180 S13: 0.0279 REMARK 3 S21: -0.3339 S22: -0.0308 S23: -0.0679 REMARK 3 S31: 0.2605 S32: 0.0383 S33: 0.0180 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 3DI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-07 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 : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38506 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 67.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : 0.45500 REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3DI0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M BIS-TRIS PH REMARK 280 6.5, 100MM PYRUVATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 60.87200 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 121.74400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.87200 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 121.74400 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.87200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 121.74400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 60.87200 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 121.74400 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: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 MET A 1 REMARK 465 GLY A 292 REMARK 465 GLU A 293 REMARK 465 ASN A 294 REMARK 465 GLU A 295 REMARK 465 GLY B 292 REMARK 465 GLU B 293 REMARK 465 ASN B 294 REMARK 465 GLU B 295 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 231 CD OE1 NE2 REMARK 480 GLU B 284 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 NE ARG B 178 O HOH B 1094 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 GLU B 284 CB GLU B 284 CG -0.147 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 267 CA - CB - CG ANGL. DEV. = -14.6 DEGREES REMARK 500 MET B 1 CG - SD - CE ANGL. DEV. = 10.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 37 16.75 83.04 REMARK 500 THR A 81 -160.24 -129.04 REMARK 500 TYR A 109 -71.88 74.09 REMARK 500 LYS A 111 -173.14 57.93 REMARK 500 ASN B 37 19.93 80.36 REMARK 500 ALA B 40 148.35 -170.29 REMARK 500 TYR B 109 -65.16 70.17 REMARK 500 LYS B 111 -173.58 61.03 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 PYR A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DI0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS DIHYDRODIPICOLINATE REMARK 900 SYNTHASE DBREF 3DI1 A 1 295 UNP Q5HG25 DAPA_STAAC 1 295 DBREF 3DI1 B 1 295 UNP Q5HG25 DAPA_STAAC 1 295 SEQRES 1 A 295 MET THR HIS LEU PHE GLU GLY VAL GLY VAL ALA LEU THR SEQRES 2 A 295 THR PRO PHE THR ASN ASN LYS VAL ASN ILE GLU ALA LEU SEQRES 3 A 295 LYS THR HIS VAL ASN PHE LEU LEU GLU ASN ASN ALA GLN SEQRES 4 A 295 ALA ILE ILE VAL ASN GLY THR THR ALA GLU SER PRO THR SEQRES 5 A 295 LEU THR THR ASP GLU LYS GLU ARG ILE LEU LYS THR VAL SEQRES 6 A 295 ILE ASP LEU VAL ASP LYS ARG VAL PRO VAL ILE ALA GLY SEQRES 7 A 295 THR GLY THR ASN ASP THR GLU LYS SER ILE GLN ALA SER SEQRES 8 A 295 ILE GLN ALA LYS ALA LEU GLY ALA ASP ALA ILE MET LEU SEQRES 9 A 295 ILE THR PRO TYR TYR ASN LYS THR ASN GLN ARG GLY LEU SEQRES 10 A 295 VAL LYS HIS PHE GLU ALA ILE ALA ASP ALA VAL LYS LEU SEQRES 11 A 295 PRO VAL VAL LEU TYR ASN VAL PRO SER ARG THR ASN MET SEQRES 12 A 295 THR ILE GLU PRO GLU THR VAL GLU ILE LEU SER GLN HIS SEQRES 13 A 295 PRO TYR ILE VAL ALA LEU LYS ASP ALA THR ASN ASP PHE SEQRES 14 A 295 GLU TYR LEU GLU GLU VAL LYS LYS ARG ILE ASP THR ASN SEQRES 15 A 295 SER PHE ALA LEU TYR SER GLY ASN ASP ASP ASN VAL VAL SEQRES 16 A 295 GLU TYR TYR GLN ARG GLY GLY GLN GLY VAL ILE SER VAL SEQRES 17 A 295 ILE ALA ASN VAL ILE PRO LYS GLU PHE GLN ALA LEU TYR SEQRES 18 A 295 ASP ALA GLN GLN SER GLY LEU ASP ILE GLN ASP GLN PHE SEQRES 19 A 295 LYS PRO ILE GLY THR LEU LEU SER ALA LEU SER VAL ASP SEQRES 20 A 295 ILE ASN PRO ILE PRO ILE LYS ALA LEU THR SER TYR LEU SEQRES 21 A 295 GLY PHE GLY ASN TYR GLU LEU ARG LEU PRO LEU VAL SER SEQRES 22 A 295 LEU GLU ASP THR ASP THR LYS VAL LEU ARG GLU THR TYR SEQRES 23 A 295 ASP THR PHE LYS ALA GLY GLU ASN GLU SEQRES 1 B 295 MET THR HIS LEU PHE GLU GLY VAL GLY VAL ALA LEU THR SEQRES 2 B 295 THR PRO PHE THR ASN ASN LYS VAL ASN ILE GLU ALA LEU SEQRES 3 B 295 LYS THR HIS VAL ASN PHE LEU LEU GLU ASN ASN ALA GLN SEQRES 4 B 295 ALA ILE ILE VAL ASN GLY THR THR ALA GLU SER PRO THR SEQRES 5 B 295 LEU THR THR ASP GLU LYS GLU ARG ILE LEU LYS THR VAL SEQRES 6 B 295 ILE ASP LEU VAL ASP LYS ARG VAL PRO VAL ILE ALA GLY SEQRES 7 B 295 THR GLY THR ASN ASP THR GLU LYS SER ILE GLN ALA SER SEQRES 8 B 295 ILE GLN ALA LYS ALA LEU GLY ALA ASP ALA ILE MET LEU SEQRES 9 B 295 ILE THR PRO TYR TYR ASN LYS THR ASN GLN ARG GLY LEU SEQRES 10 B 295 VAL LYS HIS PHE GLU ALA ILE ALA ASP ALA VAL LYS LEU SEQRES 11 B 295 PRO VAL VAL LEU TYR ASN VAL PRO SER ARG THR ASN MET SEQRES 12 B 295 THR ILE GLU PRO GLU THR VAL GLU ILE LEU SER GLN HIS SEQRES 13 B 295 PRO TYR ILE VAL ALA LEU LYS ASP ALA THR ASN ASP PHE SEQRES 14 B 295 GLU TYR LEU GLU GLU VAL LYS LYS ARG ILE ASP THR ASN SEQRES 15 B 295 SER PHE ALA LEU TYR SER GLY ASN ASP ASP ASN VAL VAL SEQRES 16 B 295 GLU TYR TYR GLN ARG GLY GLY GLN GLY VAL ILE SER VAL SEQRES 17 B 295 ILE ALA ASN VAL ILE PRO LYS GLU PHE GLN ALA LEU TYR SEQRES 18 B 295 ASP ALA GLN GLN SER GLY LEU ASP ILE GLN ASP GLN PHE SEQRES 19 B 295 LYS PRO ILE GLY THR LEU LEU SER ALA LEU SER VAL ASP SEQRES 20 B 295 ILE ASN PRO ILE PRO ILE LYS ALA LEU THR SER TYR LEU SEQRES 21 B 295 GLY PHE GLY ASN TYR GLU LEU ARG LEU PRO LEU VAL SER SEQRES 22 B 295 LEU GLU ASP THR ASP THR LYS VAL LEU ARG GLU THR TYR SEQRES 23 B 295 ASP THR PHE LYS ALA GLY GLU ASN GLU HET PYR A1001 5 HET PYR B1002 5 HETNAM PYR PYRUVIC ACID FORMUL 3 PYR 2(C3 H4 O3) FORMUL 5 HOH *238(H2 O) HELIX 1 1 ASN A 22 ASN A 36 1 15 HELIX 2 2 GLU A 49 LEU A 53 5 5 HELIX 3 3 THR A 54 ASP A 70 1 17 HELIX 4 4 ASP A 83 GLY A 98 1 16 HELIX 5 5 ASN A 113 LYS A 129 1 17 HELIX 6 6 VAL A 137 ASN A 142 1 6 HELIX 7 7 GLU A 146 GLN A 155 1 10 HELIX 8 8 ASP A 168 LYS A 177 1 10 HELIX 9 9 ASN A 190 ASP A 192 5 3 HELIX 10 10 ASN A 193 ARG A 200 1 8 HELIX 11 11 VAL A 208 VAL A 212 5 5 HELIX 12 12 ILE A 213 SER A 226 1 14 HELIX 13 13 PHE A 234 SER A 245 1 12 HELIX 14 14 PRO A 252 LEU A 260 1 9 HELIX 15 15 GLU A 275 ALA A 291 1 17 HELIX 16 16 ASN B 22 ASN B 36 1 15 HELIX 17 17 GLY B 45 LEU B 53 5 9 HELIX 18 18 THR B 54 ASP B 70 1 17 HELIX 19 19 ASP B 83 GLY B 98 1 16 HELIX 20 20 ASN B 113 LYS B 129 1 17 HELIX 21 21 VAL B 137 ASN B 142 1 6 HELIX 22 22 GLU B 146 GLN B 155 1 10 HELIX 23 23 ASP B 168 LYS B 177 1 10 HELIX 24 24 ASN B 190 ASP B 192 5 3 HELIX 25 25 ASN B 193 ARG B 200 1 8 HELIX 26 26 VAL B 208 VAL B 212 5 5 HELIX 27 27 ILE B 213 SER B 226 1 14 HELIX 28 28 PHE B 234 SER B 245 1 12 HELIX 29 29 PRO B 252 LEU B 260 1 9 HELIX 30 30 GLU B 275 ALA B 291 1 17 SHEET 1 A 9 GLY A 7 ALA A 11 0 SHEET 2 A 9 ALA A 40 VAL A 43 1 O ILE A 42 N VAL A 10 SHEET 3 A 9 VAL A 75 GLY A 78 1 O GLY A 78 N VAL A 43 SHEET 4 A 9 ALA A 101 ILE A 105 1 O MET A 103 N ALA A 77 SHEET 5 A 9 VAL A 132 ASN A 136 1 O VAL A 133 N ILE A 102 SHEET 6 A 9 ILE A 159 ASP A 164 1 O LYS A 163 N LEU A 134 SHEET 7 A 9 ALA A 185 SER A 188 1 O TYR A 187 N ASP A 164 SHEET 8 A 9 GLY A 204 SER A 207 1 O ILE A 206 N SER A 188 SHEET 9 A 9 GLY A 7 ALA A 11 1 N GLY A 9 O SER A 207 SHEET 1 B 2 PHE A 16 THR A 17 0 SHEET 2 B 2 LYS A 20 VAL A 21 -1 O LYS A 20 N THR A 17 SHEET 1 C 9 GLY B 7 ALA B 11 0 SHEET 2 C 9 ALA B 40 VAL B 43 1 O ILE B 42 N VAL B 10 SHEET 3 C 9 VAL B 75 GLY B 78 1 O GLY B 78 N VAL B 43 SHEET 4 C 9 ALA B 101 ILE B 105 1 O ALA B 101 N ALA B 77 SHEET 5 C 9 VAL B 132 ASN B 136 1 O VAL B 133 N LEU B 104 SHEET 6 C 9 ILE B 159 ASP B 164 1 O LYS B 163 N LEU B 134 SHEET 7 C 9 ALA B 185 SER B 188 1 O TYR B 187 N ASP B 164 SHEET 8 C 9 GLY B 204 SER B 207 1 O ILE B 206 N SER B 188 SHEET 9 C 9 GLY B 7 ALA B 11 1 N GLY B 9 O SER B 207 SHEET 1 D 2 PHE B 16 THR B 17 0 SHEET 2 D 2 LYS B 20 VAL B 21 -1 O LYS B 20 N THR B 17 LINK NZ LYS A 163 CA PYR A1001 1555 1555 1.34 LINK NZ LYS B 163 CA PYR B1002 1555 1555 1.35 CISPEP 1 ASN A 249 PRO A 250 0 2.83 CISPEP 2 LEU A 269 PRO A 270 0 16.34 CISPEP 3 ASN B 249 PRO B 250 0 3.89 CISPEP 4 LEU B 269 PRO B 270 0 15.42 SITE 1 AC1 7 ALA A 11 GLY A 45 THR A 46 THR A 47 SITE 2 AC1 7 MET A 103 TYR A 135 LYS A 163 SITE 1 AC2 6 ALA B 11 GLY B 45 THR B 46 THR B 47 SITE 2 AC2 6 TYR B 135 LYS B 163 CRYST1 117.440 117.440 182.616 90.00 90.00 120.00 P 64 2 2 24 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 0.008515 0.004916 0.000000 0.00000 SCALE2 0.000000 0.009832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005476 0.00000