HEADER LYASE 01-SEP-06 2I8C TITLE ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D-ALANINE TITLE 2 LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE-D-ALANINE LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D-ALANYLALANINE SYNTHETASE, D-ALA-D-ALA LIGASE; COMPND 5 EC: 6.3.2.4; 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: DDL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-60 KEYWDS D-ALANINE:D-ALANINE LIGASE, ADP COMPLEX, STAPHYLOCOCCUS AUREUS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,J.S.CHANG,J.T.HERBERG,M.HORNG,P.K.TOMICH,A.H.LIN,K.R.MAROTTI REVDAT 5 30-AUG-23 2I8C 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2I8C 1 VERSN REVDAT 3 24-FEB-09 2I8C 1 VERSN REVDAT 2 24-OCT-06 2I8C 1 JRNL REVDAT 1 26-SEP-06 2I8C 0 JRNL AUTH S.LIU,J.S.CHANG,J.T.HERBERG,M.M.HORNG,P.K.TOMICH,A.H.LIN, JRNL AUTH 2 K.R.MAROTTI JRNL TITL ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS JRNL TITL 2 D-ALANINE:D-ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC JRNL TITL 3 STUDIES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 15178 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17015835 JRNL DOI 10.1073/PNAS.0604905103 REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0008 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 23741 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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) : 2.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 40.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -2.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.329 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.820 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5669 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3775 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7684 ; 1.776 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9286 ; 0.981 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 688 ; 7.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;42.023 ;25.971 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1002 ;19.356 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;21.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 849 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6256 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1050 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1320 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3834 ; 0.206 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2701 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3081 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 127 ; 0.152 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.091 ; 0.200 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): 30 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.191 ; 0.200 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): 4359 ; 1.049 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1395 ; 0.156 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5558 ; 1.262 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2551 ; 2.019 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2126 ; 3.000 ; 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 : 6 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 125 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0618 0.1384 -5.1667 REMARK 3 T TENSOR REMARK 3 T11: -0.1046 T22: -0.1077 REMARK 3 T33: -0.0408 T12: 0.0077 REMARK 3 T13: 0.0813 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.7808 L22: 1.3270 REMARK 3 L33: 5.7606 L12: 0.2724 REMARK 3 L13: -1.1879 L23: -0.2377 REMARK 3 S TENSOR REMARK 3 S11: -0.1226 S12: 0.2375 S13: -0.2388 REMARK 3 S21: -0.1696 S22: -0.1002 S23: -0.2294 REMARK 3 S31: 0.4059 S32: 0.1284 S33: 0.2229 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 : A 126 A 219 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8604 -17.0895 21.1107 REMARK 3 T TENSOR REMARK 3 T11: -0.0534 T22: -0.1045 REMARK 3 T33: -0.1024 T12: -0.1061 REMARK 3 T13: 0.0012 T23: -0.0520 REMARK 3 L TENSOR REMARK 3 L11: 3.5157 L22: 3.7927 REMARK 3 L33: 3.0962 L12: -0.7930 REMARK 3 L13: 1.5560 L23: -1.7869 REMARK 3 S TENSOR REMARK 3 S11: 0.1224 S12: 0.0544 S13: -0.2991 REMARK 3 S21: -0.0020 S22: 0.1666 S23: 0.0634 REMARK 3 S31: 0.5358 S32: -0.3884 S33: -0.2890 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 220 A 358 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8683 1.6629 3.2677 REMARK 3 T TENSOR REMARK 3 T11: -0.1865 T22: 0.0140 REMARK 3 T33: -0.0222 T12: 0.0280 REMARK 3 T13: -0.0032 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 4.4132 L22: 2.3930 REMARK 3 L33: 2.3071 L12: 2.1474 REMARK 3 L13: -1.0320 L23: -0.5962 REMARK 3 S TENSOR REMARK 3 S11: -0.0038 S12: 0.3594 S13: 0.0502 REMARK 3 S21: -0.0875 S22: 0.0048 S23: 0.1813 REMARK 3 S31: 0.0007 S32: -0.4556 S33: -0.0010 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 125 REMARK 3 ORIGIN FOR THE GROUP (A): 42.5439 2.6099 17.4732 REMARK 3 T TENSOR REMARK 3 T11: -0.1370 T22: 0.0406 REMARK 3 T33: 0.0098 T12: -0.0793 REMARK 3 T13: -0.0128 T23: 0.1539 REMARK 3 L TENSOR REMARK 3 L11: 5.4258 L22: 1.5517 REMARK 3 L33: 5.1590 L12: -0.1139 REMARK 3 L13: 0.4286 L23: 1.0388 REMARK 3 S TENSOR REMARK 3 S11: -0.0993 S12: 0.5111 S13: 0.4058 REMARK 3 S21: -0.1618 S22: -0.1086 S23: -0.1511 REMARK 3 S31: -0.6578 S32: 0.8387 S33: 0.2079 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 126 B 219 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9971 15.0435 26.7164 REMARK 3 T TENSOR REMARK 3 T11: -0.0474 T22: -0.1404 REMARK 3 T33: -0.0831 T12: 0.0417 REMARK 3 T13: 0.0001 T23: -0.0728 REMARK 3 L TENSOR REMARK 3 L11: 1.5515 L22: 3.8327 REMARK 3 L33: 4.2450 L12: -1.4914 REMARK 3 L13: 0.6239 L23: -0.4549 REMARK 3 S TENSOR REMARK 3 S11: -0.1479 S12: -0.0320 S13: 0.1087 REMARK 3 S21: -0.0112 S22: 0.1126 S23: 0.0325 REMARK 3 S31: -0.4705 S32: -0.3250 S33: 0.0353 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 220 B 360 REMARK 3 ORIGIN FOR THE GROUP (A): 28.6281 -2.7546 33.3310 REMARK 3 T TENSOR REMARK 3 T11: -0.0274 T22: -0.1511 REMARK 3 T33: -0.0992 T12: 0.0132 REMARK 3 T13: -0.0255 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 2.4116 L22: 2.3253 REMARK 3 L33: 3.5670 L12: -0.8824 REMARK 3 L13: -0.5849 L23: 1.1119 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: -0.0219 S13: -0.0648 REMARK 3 S21: 0.2654 S22: -0.1238 S23: -0.1483 REMARK 3 S31: -0.0070 S32: 0.0930 S33: 0.1262 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2I8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23741 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 79.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.62100 REMARK 200 R SYM FOR SHELL (I) : 0.62100 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2I87 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 33.48600 REMARK 290 SMTRY3 2 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: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 THR A 2 REMARK 465 TYR A 246 REMARK 465 ASP A 247 REMARK 465 TYR A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 LYS A 251 REMARK 465 TYR A 252 REMARK 465 LYS A 253 REMARK 465 ASP A 254 REMARK 465 GLY A 255 REMARK 465 LYS A 256 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 465 HIS A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 TYR B 246 REMARK 465 ASP B 247 REMARK 465 TYR B 248 REMARK 465 LYS B 249 REMARK 465 SER B 250 REMARK 465 LYS B 251 REMARK 465 TYR B 252 REMARK 465 LYS B 253 REMARK 465 ASP B 254 REMARK 465 GLY B 255 REMARK 465 LYS B 256 REMARK 465 HIS B 361 REMARK 465 HIS B 362 REMARK 465 HIS B 363 REMARK 465 HIS B 364 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 GLU A 16 9.53 -65.96 REMARK 500 ASN A 54 75.28 48.70 REMARK 500 LEU A 67 -108.85 56.41 REMARK 500 ASN A 69 47.99 -104.40 REMARK 500 LEU A 94 65.13 -112.49 REMARK 500 LEU A 95 74.82 -153.87 REMARK 500 HIS A 96 -113.09 -3.03 REMARK 500 PRO A 98 -147.59 -29.71 REMARK 500 ASP A 113 31.33 73.20 REMARK 500 SER A 184 -136.81 -150.51 REMARK 500 ASN A 228 -88.95 -107.62 REMARK 500 ASP A 299 39.64 -99.37 REMARK 500 ASN A 305 -60.09 -93.87 REMARK 500 ASN B 45 46.87 -77.58 REMARK 500 ASP B 46 4.74 -151.65 REMARK 500 ASN B 54 74.92 50.36 REMARK 500 GLU B 58 55.39 -90.47 REMARK 500 ILE B 59 106.82 -11.46 REMARK 500 LEU B 73 171.10 -59.40 REMARK 500 HIS B 96 -62.88 -19.14 REMARK 500 ASN B 99 101.62 55.54 REMARK 500 GLU B 101 -165.26 47.21 REMARK 500 SER B 183 68.88 -65.00 REMARK 500 VAL B 185 -159.57 -85.53 REMARK 500 SER B 188 144.66 -173.14 REMARK 500 ASN B 228 -88.60 -114.45 REMARK 500 ASP B 264 78.46 -67.04 REMARK 500 PHE B 313 22.21 -140.97 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 SER A 184 VAL A 185 -148.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 306 OE2 REMARK 620 2 ADP B 400 O2A 70.6 REMARK 620 3 ADP B 400 O2B 114.7 94.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I80 RELATED DB: PDB REMARK 900 ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D-ALANINE REMARK 900 LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES REMARK 900 RELATED ID: 2I87 RELATED DB: PDB REMARK 900 ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D-ALANINE REMARK 900 LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES DBREF 2I8C A 1 356 UNP Q5HEB7 DDL_STAAC 1 356 DBREF 2I8C B 1 356 UNP Q5HEB7 DDL_STAAC 1 356 SEQADV 2I8C ARG A 357 UNP Q5HEB7 CLONING ARTIFACT SEQADV 2I8C SER A 358 UNP Q5HEB7 CLONING ARTIFACT SEQADV 2I8C HIS A 359 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS A 360 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS A 361 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS A 362 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS A 363 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS A 364 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C ARG B 357 UNP Q5HEB7 CLONING ARTIFACT SEQADV 2I8C SER B 358 UNP Q5HEB7 CLONING ARTIFACT SEQADV 2I8C HIS B 359 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS B 360 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS B 361 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS B 362 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS B 363 UNP Q5HEB7 EXPRESSION TAG SEQADV 2I8C HIS B 364 UNP Q5HEB7 EXPRESSION TAG SEQRES 1 A 364 MET THR LYS GLU ASN ILE CYS ILE VAL PHE GLY GLY LYS SEQRES 2 A 364 SER ALA GLU HIS GLU VAL SER ILE LEU THR ALA GLN ASN SEQRES 3 A 364 VAL LEU ASN ALA ILE ASP LYS ASP LYS TYR HIS VAL ASP SEQRES 4 A 364 ILE ILE TYR ILE THR ASN ASP GLY ASP TRP ARG LYS GLN SEQRES 5 A 364 ASN ASN ILE THR ALA GLU ILE LYS SER THR ASP GLU LEU SEQRES 6 A 364 HIS LEU GLU ASN GLY GLU ALA LEU GLU ILE SER GLN LEU SEQRES 7 A 364 LEU LYS GLU SER SER SER GLY GLN PRO TYR ASP ALA VAL SEQRES 8 A 364 PHE PRO LEU LEU HIS GLY PRO ASN GLY GLU ASP GLY THR SEQRES 9 A 364 ILE GLN GLY LEU PHE GLU VAL LEU ASP VAL PRO TYR VAL SEQRES 10 A 364 GLY ASN GLY VAL LEU SER ALA ALA SER SER MET ASP LYS SEQRES 11 A 364 LEU VAL MET LYS GLN LEU PHE GLU HIS ARG GLY LEU PRO SEQRES 12 A 364 GLN LEU PRO TYR ILE SER PHE LEU ARG SER GLU TYR GLU SEQRES 13 A 364 LYS TYR GLU HIS ASN ILE LEU LYS LEU VAL ASN ASP LYS SEQRES 14 A 364 LEU ASN TYR PRO VAL PHE VAL LYS PRO ALA ASN LEU GLY SEQRES 15 A 364 SER SER VAL GLY ILE SER LYS CYS ASN ASN GLU ALA GLU SEQRES 16 A 364 LEU LYS GLU GLY ILE LYS GLU ALA PHE GLN PHE ASP ARG SEQRES 17 A 364 LYS LEU VAL ILE GLU GLN GLY VAL ASN ALA ARG GLU ILE SEQRES 18 A 364 GLU VAL ALA VAL LEU GLY ASN ASP TYR PRO GLU ALA THR SEQRES 19 A 364 TRP PRO GLY GLU VAL VAL LYS ASP VAL ALA PHE TYR ASP SEQRES 20 A 364 TYR LYS SER LYS TYR LYS ASP GLY LYS VAL GLN LEU GLN SEQRES 21 A 364 ILE PRO ALA ASP LEU ASP GLU ASP VAL GLN LEU THR LEU SEQRES 22 A 364 ARG ASN MET ALA LEU GLU ALA PHE LYS ALA THR ASP CYS SEQRES 23 A 364 SER GLY LEU VAL ARG ALA ASP PHE PHE VAL THR GLU ASP SEQRES 24 A 364 ASN GLN ILE TYR ILE ASN GLU THR ASN ALA MET PRO GLY SEQRES 25 A 364 PHE THR ALA PHE SER MET TYR PRO LYS LEU TRP GLU ASN SEQRES 26 A 364 MET GLY LEU SER TYR PRO GLU LEU ILE THR LYS LEU ILE SEQRES 27 A 364 GLU LEU ALA LYS GLU ARG HIS GLN ASP LYS GLN LYS ASN SEQRES 28 A 364 LYS TYR LYS ILE ASP ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 364 MET THR LYS GLU ASN ILE CYS ILE VAL PHE GLY GLY LYS SEQRES 2 B 364 SER ALA GLU HIS GLU VAL SER ILE LEU THR ALA GLN ASN SEQRES 3 B 364 VAL LEU ASN ALA ILE ASP LYS ASP LYS TYR HIS VAL ASP SEQRES 4 B 364 ILE ILE TYR ILE THR ASN ASP GLY ASP TRP ARG LYS GLN SEQRES 5 B 364 ASN ASN ILE THR ALA GLU ILE LYS SER THR ASP GLU LEU SEQRES 6 B 364 HIS LEU GLU ASN GLY GLU ALA LEU GLU ILE SER GLN LEU SEQRES 7 B 364 LEU LYS GLU SER SER SER GLY GLN PRO TYR ASP ALA VAL SEQRES 8 B 364 PHE PRO LEU LEU HIS GLY PRO ASN GLY GLU ASP GLY THR SEQRES 9 B 364 ILE GLN GLY LEU PHE GLU VAL LEU ASP VAL PRO TYR VAL SEQRES 10 B 364 GLY ASN GLY VAL LEU SER ALA ALA SER SER MET ASP LYS SEQRES 11 B 364 LEU VAL MET LYS GLN LEU PHE GLU HIS ARG GLY LEU PRO SEQRES 12 B 364 GLN LEU PRO TYR ILE SER PHE LEU ARG SER GLU TYR GLU SEQRES 13 B 364 LYS TYR GLU HIS ASN ILE LEU LYS LEU VAL ASN ASP LYS SEQRES 14 B 364 LEU ASN TYR PRO VAL PHE VAL LYS PRO ALA ASN LEU GLY SEQRES 15 B 364 SER SER VAL GLY ILE SER LYS CYS ASN ASN GLU ALA GLU SEQRES 16 B 364 LEU LYS GLU GLY ILE LYS GLU ALA PHE GLN PHE ASP ARG SEQRES 17 B 364 LYS LEU VAL ILE GLU GLN GLY VAL ASN ALA ARG GLU ILE SEQRES 18 B 364 GLU VAL ALA VAL LEU GLY ASN ASP TYR PRO GLU ALA THR SEQRES 19 B 364 TRP PRO GLY GLU VAL VAL LYS ASP VAL ALA PHE TYR ASP SEQRES 20 B 364 TYR LYS SER LYS TYR LYS ASP GLY LYS VAL GLN LEU GLN SEQRES 21 B 364 ILE PRO ALA ASP LEU ASP GLU ASP VAL GLN LEU THR LEU SEQRES 22 B 364 ARG ASN MET ALA LEU GLU ALA PHE LYS ALA THR ASP CYS SEQRES 23 B 364 SER GLY LEU VAL ARG ALA ASP PHE PHE VAL THR GLU ASP SEQRES 24 B 364 ASN GLN ILE TYR ILE ASN GLU THR ASN ALA MET PRO GLY SEQRES 25 B 364 PHE THR ALA PHE SER MET TYR PRO LYS LEU TRP GLU ASN SEQRES 26 B 364 MET GLY LEU SER TYR PRO GLU LEU ILE THR LYS LEU ILE SEQRES 27 B 364 GLU LEU ALA LYS GLU ARG HIS GLN ASP LYS GLN LYS ASN SEQRES 28 B 364 LYS TYR LYS ILE ASP ARG SER HIS HIS HIS HIS HIS HIS HET SO4 A 401 5 HET ADP A 400 27 HET SO4 B 401 5 HET MG B 402 1 HET ADP B 400 27 HETNAM SO4 SULFATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 6 MG MG 2+ HELIX 1 1 GLU A 16 ALA A 30 1 15 HELIX 2 2 SER A 61 LEU A 65 5 5 HELIX 3 3 HIS A 66 GLY A 70 5 5 HELIX 4 4 SER A 76 GLU A 81 5 6 HELIX 5 5 GLY A 103 ASP A 113 1 11 HELIX 6 6 GLY A 120 MET A 128 1 9 HELIX 7 7 ASP A 129 GLY A 141 1 13 HELIX 8 8 ARG A 152 TYR A 158 1 7 HELIX 9 9 TYR A 158 LEU A 170 1 13 HELIX 10 10 ASN A 192 PHE A 204 1 13 HELIX 11 11 ASP A 266 THR A 284 1 19 HELIX 12 12 SER A 317 MET A 326 1 10 HELIX 13 13 SER A 329 ARG A 357 1 29 HELIX 14 14 GLU B 16 ILE B 31 1 16 HELIX 15 15 GLU B 74 GLU B 81 1 8 HELIX 16 16 GLY B 103 LEU B 112 1 10 HELIX 17 17 GLY B 120 SER B 127 1 8 HELIX 18 18 ASP B 129 GLY B 141 1 13 HELIX 19 19 ARG B 152 LEU B 170 1 19 HELIX 20 20 ASN B 192 GLN B 205 1 14 HELIX 21 21 ASP B 266 THR B 284 1 19 HELIX 22 22 SER B 317 MET B 326 1 10 HELIX 23 23 SER B 329 SER B 358 1 30 SHEET 1 A 5 GLU A 71 ALA A 72 0 SHEET 2 A 5 TRP A 49 ILE A 55 -1 N LYS A 51 O GLU A 71 SHEET 3 A 5 TYR A 36 ILE A 43 -1 N TYR A 42 O ARG A 50 SHEET 4 A 5 GLU A 4 GLY A 11 1 N GLU A 4 O HIS A 37 SHEET 5 A 5 ALA A 90 LEU A 94 1 O LEU A 94 N VAL A 9 SHEET 1 B 4 TYR A 147 LEU A 151 0 SHEET 2 B 4 LYS A 209 GLN A 214 -1 O ILE A 212 N ILE A 148 SHEET 3 B 4 VAL A 174 PRO A 178 -1 N LYS A 177 O VAL A 211 SHEET 4 B 4 SER A 188 CYS A 190 -1 O CYS A 190 N VAL A 174 SHEET 1 C 4 GLU A 232 ALA A 233 0 SHEET 2 C 4 ARG A 219 GLY A 227 -1 N LEU A 226 O GLU A 232 SHEET 3 C 4 GLY A 237 VAL A 239 -1 O GLY A 237 N GLU A 222 SHEET 4 C 4 LEU A 259 GLN A 260 -1 O GLN A 260 N GLU A 238 SHEET 1 D 4 GLU A 232 ALA A 233 0 SHEET 2 D 4 ARG A 219 GLY A 227 -1 N LEU A 226 O GLU A 232 SHEET 3 D 4 GLY A 288 VAL A 296 -1 O PHE A 294 N ILE A 221 SHEET 4 D 4 ILE A 302 ASN A 308 -1 O TYR A 303 N PHE A 295 SHEET 1 E 4 ARG B 50 GLN B 52 0 SHEET 2 E 4 TYR B 36 ILE B 43 -1 N TYR B 42 O ARG B 50 SHEET 3 E 4 GLU B 4 GLY B 11 1 N ILE B 6 O HIS B 37 SHEET 4 E 4 ALA B 90 PRO B 93 1 O PHE B 92 N CYS B 7 SHEET 1 F 4 TYR B 147 LEU B 151 0 SHEET 2 F 4 LYS B 209 GLN B 214 -1 O ILE B 212 N ILE B 148 SHEET 3 F 4 VAL B 174 PRO B 178 -1 N PHE B 175 O GLU B 213 SHEET 4 F 4 SER B 188 CYS B 190 -1 O SER B 188 N VAL B 176 SHEET 1 G 4 GLU B 232 ALA B 233 0 SHEET 2 G 4 ARG B 219 GLY B 227 -1 N LEU B 226 O GLU B 232 SHEET 3 G 4 GLY B 237 VAL B 239 -1 O GLY B 237 N GLU B 222 SHEET 4 G 4 LEU B 259 GLN B 260 -1 O GLN B 260 N GLU B 238 SHEET 1 H 4 GLU B 232 ALA B 233 0 SHEET 2 H 4 ARG B 219 GLY B 227 -1 N LEU B 226 O GLU B 232 SHEET 3 H 4 GLY B 288 VAL B 296 -1 O VAL B 296 N ARG B 219 SHEET 4 H 4 ILE B 302 ASN B 308 -1 O GLU B 306 N ASP B 293 LINK OE2 GLU B 306 MG MG B 402 1555 1555 2.19 LINK O2A ADP B 400 MG MG B 402 1555 1555 2.21 LINK O2B ADP B 400 MG MG B 402 1555 1555 2.10 CISPEP 1 TYR A 172 PRO A 173 0 3.85 CISPEP 2 ILE A 261 PRO A 262 0 -3.34 CISPEP 3 TYR B 172 PRO B 173 0 -2.26 CISPEP 4 ILE B 261 PRO B 262 0 -6.74 SITE 1 AC1 4 HIS A 96 ARG A 291 ASN A 308 GLY A 312 SITE 1 AC2 3 ARG B 291 ASN B 308 GLY B 312 SITE 1 AC3 2 GLU B 306 ADP B 400 SITE 1 AC4 12 LYS A 130 LEU A 145 PHE A 175 LYS A 177 SITE 2 AC4 12 SER A 183 GLU A 213 GLN A 214 GLY A 215 SITE 3 AC4 12 VAL A 216 GLU A 220 ASN A 305 GLU A 306 SITE 1 AC5 12 PHE B 175 LYS B 177 SER B 183 GLU B 213 SITE 2 AC5 12 GLN B 214 GLY B 215 VAL B 216 GLU B 220 SITE 3 AC5 12 PHE B 295 ASN B 305 GLU B 306 MG B 402 CRYST1 67.802 66.972 78.992 90.00 96.05 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 0.014749 0.000000 0.001563 0.00000 SCALE2 0.000000 0.014932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012730 0.00000