HEADER PEPTIDE BINDING PROTEIN/PEPTIDE 04-AUG-10 3O9P TITLE THE STRUCTURE OF THE ESCHERICHIA COLI MUREIN TRIPEPTIDE BINDING TITLE 2 PROTEIN MPPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC MUREIN PEPTIDE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 23-537; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: B1329, JW1322, MPPA, YNAH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC KEYWDS OLIGOPEPTIDE BINDING PROTEINS, MUREIN TRIPEPTIDE, PERIPLASMIC KEYWDS 2 PROTEIN, PEPTIDE BINDING PROTEIN-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MAQBOOL,V.M.LEVDIKOV,E.V.BLAGOVA,A.J.WILKINSON,G.H.THOMAS REVDAT 4 06-SEP-23 3O9P 1 REMARK SEQADV LINK REVDAT 3 21-SEP-11 3O9P 1 JRNL REVDAT 2 14-SEP-11 3O9P 1 JRNL VERSN REVDAT 1 06-JUL-11 3O9P 0 JRNL AUTH A.MAQBOOL,V.M.LEVDIKOV,E.V.BLAGOVA,M.HERVE,R.S.HORLER, JRNL AUTH 2 A.J.WILKINSON,G.H.THOMAS JRNL TITL COMPENSATING STEREOCHEMICAL CHANGES ALLOW MUREIN TRIPEPTIDE JRNL TITL 2 TO BE ACCOMMODATED IN A CONVENTIONAL PEPTIDE-BINDING JRNL TITL 3 PROTEIN. JRNL REF J.BIOL.CHEM. V. 286 31512 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21705338 JRNL DOI 10.1074/JBC.M111.267179 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32850 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1743 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 338 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : -0.01000 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): 0.195 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.385 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4176 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2800 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5696 ; 1.896 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6865 ; 1.022 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 6.175 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 190 ;37.593 ;25.053 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 689 ;15.318 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.974 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 633 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4630 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 805 ; 0.001 ; 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): 2554 ; 3.092 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1012 ; 1.123 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4149 ; 4.380 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1622 ; 6.107 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1546 ; 7.858 ;10.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3O9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-09 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9350 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: PDB ENTRY 2Z23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 50MM ZINC ACETATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 115610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -787.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 ALA A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 SER A 5 REMARK 465 GLY A 6 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 O HIS A 515 O HOH A 849 2.14 REMARK 500 OD2 ASP A 78 O HOH A 632 2.16 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 433 CB SER A 433 OG -0.102 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 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 140 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 297 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 460 NE - CZ - NH2 ANGL. DEV. = -4.3 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 ASN A 69 14.09 57.08 REMARK 500 GLU A 199 -50.08 -127.97 REMARK 500 SER A 245 -174.13 65.82 REMARK 500 THR A 264 47.69 -142.80 REMARK 500 LEU A 305 -80.00 -109.55 REMARK 500 LYS A 355 85.47 -175.51 REMARK 500 SER A 366 139.95 177.88 REMARK 500 ASN A 435 78.66 -66.16 REMARK 500 ALA A 475 52.54 38.22 REMARK 500 ILE A 480 -59.08 -121.74 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 ZN A 517 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 142 NE2 REMARK 620 2 HOH A 694 O 103.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 518 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 208 NE2 REMARK 620 2 HOH A 752 O 88.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 519 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 314 NE2 REMARK 620 2 ASP A 318 OD1 96.1 REMARK 620 3 HOH A 649 O 103.6 92.8 REMARK 620 4 HOH A 654 O 114.8 118.9 125.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 520 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 515 NE2 REMARK 620 2 HOH A 521 O 94.2 REMARK 620 3 HOH A 795 O 87.3 167.5 REMARK 620 4 HOH A 858 O 107.1 107.7 83.6 REMARK 620 N 1 2 3 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 MHI A 516 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ALA DGL API REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MHI A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 520 DBREF 3O9P A 1 515 UNP P77348 MPPA_ECOLI 23 537 SEQADV 3O9P GLY A -3 UNP P77348 EXPRESSION TAG SEQADV 3O9P PRO A -2 UNP P77348 EXPRESSION TAG SEQADV 3O9P ALA A -1 UNP P77348 EXPRESSION TAG SEQADV 3O9P MET A 0 UNP P77348 EXPRESSION TAG SEQRES 1 A 519 GLY PRO ALA MET ALA GLU VAL PRO SER GLY THR VAL LEU SEQRES 2 A 519 ALA GLU LYS GLN GLU LEU VAL ARG HIS ILE LYS ASP GLU SEQRES 3 A 519 PRO ALA SER LEU ASP PRO ALA LYS ALA VAL GLY LEU PRO SEQRES 4 A 519 GLU ILE GLN VAL ILE ARG ASP LEU PHE GLU GLY LEU VAL SEQRES 5 A 519 ASN GLN ASN GLU LYS GLY GLU ILE VAL PRO GLY VAL ALA SEQRES 6 A 519 THR GLN TRP LYS SER ASN ASP ASN ARG ILE TRP THR PHE SEQRES 7 A 519 THR LEU ARG ASP ASN ALA LYS TRP ALA ASP GLY THR PRO SEQRES 8 A 519 VAL THR ALA GLN ASP PHE VAL TYR SER TRP GLN ARG LEU SEQRES 9 A 519 VAL ASP PRO LYS THR LEU SER PRO PHE ALA TRP PHE ALA SEQRES 10 A 519 ALA LEU ALA GLY ILE ASN ASN ALA GLN ALA ILE ILE ASP SEQRES 11 A 519 GLY LYS ALA THR PRO ASP GLN LEU GLY VAL THR ALA VAL SEQRES 12 A 519 ASP ALA HIS THR LEU LYS ILE GLN LEU ASP LYS PRO LEU SEQRES 13 A 519 PRO TRP PHE VAL ASN LEU THR ALA ASN PHE ALA PHE PHE SEQRES 14 A 519 PRO VAL GLN LYS ALA ASN VAL GLU SER GLY LYS GLU TRP SEQRES 15 A 519 THR LYS PRO GLY ASN LEU ILE GLY ASN GLY ALA TYR VAL SEQRES 16 A 519 LEU LYS GLU ARG VAL VAL ASN GLU LYS LEU VAL VAL VAL SEQRES 17 A 519 PRO ASN THR HIS TYR TRP ASP ASN ALA LYS THR VAL LEU SEQRES 18 A 519 GLN LYS VAL THR PHE LEU PRO ILE ASN GLN GLU SER ALA SEQRES 19 A 519 ALA THR LYS ARG TYR LEU ALA GLY ASP ILE ASP ILE THR SEQRES 20 A 519 GLU SER PHE PRO LYS ASN MET TYR GLN LYS LEU LEU LYS SEQRES 21 A 519 ASP ILE PRO GLY GLN VAL TYR THR PRO PRO GLN LEU GLY SEQRES 22 A 519 THR TYR TYR TYR ALA PHE ASN THR GLN LYS GLY PRO THR SEQRES 23 A 519 ALA ASP GLN ARG VAL ARG LEU ALA LEU SER MET THR ILE SEQRES 24 A 519 ASP ARG ARG LEU MET THR GLU LYS VAL LEU GLY THR GLY SEQRES 25 A 519 GLU LYS PRO ALA TRP HIS PHE THR PRO ASP VAL THR ALA SEQRES 26 A 519 GLY PHE THR PRO GLU PRO SER PRO PHE GLU GLN MET SER SEQRES 27 A 519 GLN GLU GLU LEU ASN ALA GLN ALA LYS THR LEU LEU SER SEQRES 28 A 519 ALA ALA GLY TYR GLY PRO GLN LYS PRO LEU LYS LEU THR SEQRES 29 A 519 LEU LEU TYR ASN THR SER GLU ASN HIS GLN LYS ILE ALA SEQRES 30 A 519 ILE ALA VAL ALA SER MET TRP LYS LYS ASN LEU GLY VAL SEQRES 31 A 519 ASP VAL LYS LEU GLN ASN GLN GLU TRP LYS THR TYR ILE SEQRES 32 A 519 ASP SER ARG ASN THR GLY ASN PHE ASP VAL ILE ARG ALA SEQRES 33 A 519 SER TRP VAL GLY ASP TYR ASN GLU PRO SER THR PHE LEU SEQRES 34 A 519 THR LEU LEU THR SER THR HIS SER GLY ASN ILE SER ARG SEQRES 35 A 519 PHE ASN ASN PRO ALA TYR ASP LYS VAL LEU ALA GLN ALA SEQRES 36 A 519 SER THR GLU ASN THR VAL LYS ALA ARG ASN ALA ASP TYR SEQRES 37 A 519 ASN ALA ALA GLU LYS ILE LEU MET GLU GLN ALA PRO ILE SEQRES 38 A 519 ALA PRO ILE TYR GLN TYR THR ASN GLY ARG LEU ILE LYS SEQRES 39 A 519 PRO TRP LEU LYS GLY TYR PRO ILE ASN ASN PRO GLU ASP SEQRES 40 A 519 VAL ALA TYR SER ARG THR MET TYR ILE VAL LYS HIS HET MHI A 516 27 HET ZN A 517 1 HET ZN A 518 1 HET ZN A 519 1 HET ZN A 520 1 HETNAM MHI L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID HETNAM ZN ZINC ION FORMUL 2 MHI C15 H26 N4 O8 FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *338(H2 O) HELIX 1 1 GLY A 33 PHE A 44 1 12 HELIX 2 2 THR A 89 ASP A 102 1 14 HELIX 3 3 PRO A 103 LEU A 106 5 4 HELIX 4 4 ALA A 110 GLY A 117 1 8 HELIX 5 5 ASN A 120 ASP A 126 1 7 HELIX 6 6 THR A 130 LEU A 134 5 5 HELIX 7 7 TRP A 154 ALA A 160 1 7 HELIX 8 8 ASN A 161 PHE A 165 5 5 HELIX 9 9 GLN A 168 SER A 174 1 7 HELIX 10 10 ASP A 211 THR A 215 5 5 HELIX 11 11 GLN A 227 ALA A 237 1 11 HELIX 12 12 PRO A 247 ASN A 249 5 3 HELIX 13 13 MET A 250 ILE A 258 1 9 HELIX 14 14 GLY A 280 ALA A 283 5 4 HELIX 15 15 ASP A 284 ILE A 295 1 12 HELIX 16 16 ASP A 296 VAL A 304 1 9 HELIX 17 17 SER A 328 MET A 333 1 6 HELIX 18 18 SER A 334 GLY A 350 1 17 HELIX 19 19 SER A 366 GLY A 385 1 20 HELIX 20 20 GLU A 394 ARG A 402 1 9 HELIX 21 21 PRO A 421 THR A 426 1 6 HELIX 22 22 LEU A 427 THR A 429 5 3 HELIX 23 23 ASN A 441 SER A 452 1 12 HELIX 24 24 THR A 456 ALA A 475 1 20 HELIX 25 25 TYR A 506 MET A 510 5 5 SHEET 1 A 4 GLU A 14 ILE A 19 0 SHEET 2 A 4 LYS A 219 PRO A 224 1 O THR A 221 N LEU A 15 SHEET 3 A 4 LYS A 200 PRO A 205 -1 N LEU A 201 O PHE A 222 SHEET 4 A 4 TYR A 190 VAL A 196 -1 N GLU A 194 O VAL A 202 SHEET 1 B 2 VAL A 48 GLN A 50 0 SHEET 2 B 2 ILE A 56 PRO A 58 -1 O VAL A 57 N ASN A 49 SHEET 1 C 4 ALA A 61 LYS A 65 0 SHEET 2 C 4 ILE A 71 LEU A 76 -1 O THR A 73 N LYS A 65 SHEET 3 C 4 THR A 143 GLN A 147 -1 O LEU A 144 N PHE A 74 SHEET 4 C 4 VAL A 136 ASP A 140 -1 N THR A 137 O LYS A 145 SHEET 1 D 2 VAL A 262 TYR A 263 0 SHEET 2 D 2 ARG A 487 LEU A 488 -1 O ARG A 487 N TYR A 263 SHEET 1 E 6 LYS A 310 PRO A 311 0 SHEET 2 E 6 ILE A 477 THR A 484 -1 O GLN A 482 N LYS A 310 SHEET 3 E 6 PRO A 266 PHE A 275 -1 N TYR A 273 O ALA A 478 SHEET 4 E 6 VAL A 409 VAL A 415 -1 O ILE A 410 N ALA A 274 SHEET 5 E 6 LYS A 358 ASN A 364 1 N LEU A 362 O ARG A 411 SHEET 6 E 6 ASP A 387 GLN A 393 1 O LYS A 389 N LEU A 359 SHEET 1 F 2 LEU A 493 LYS A 494 0 SHEET 2 F 2 TYR A 511 ILE A 512 -1 O TYR A 511 N LYS A 494 LINK NE2 HIS A 142 ZN ZN A 517 1555 1555 2.13 LINK NE2 HIS A 208 ZN ZN A 518 1555 1555 2.10 LINK NE2 HIS A 314 ZN ZN A 519 1555 1555 2.17 LINK OD1 ASP A 318 ZN ZN A 519 1555 1555 2.05 LINK NE2 HIS A 515 ZN ZN A 520 1555 1555 2.19 LINK ZN ZN A 517 O HOH A 694 1555 1555 1.76 LINK ZN ZN A 518 O HOH A 752 1555 1555 1.95 LINK ZN ZN A 519 O HOH A 649 1555 1555 2.40 LINK ZN ZN A 519 O HOH A 654 1555 1555 2.33 LINK ZN ZN A 520 O HOH A 521 1555 1555 2.54 LINK ZN ZN A 520 O HOH A 795 1555 1555 2.43 LINK ZN ZN A 520 O HOH A 858 1555 1555 1.79 SITE 1 AC1 23 LYS A 20 VAL A 32 LEU A 34 ILE A 37 SITE 2 AC1 23 GLN A 267 ARG A 402 ARG A 411 SER A 413 SITE 3 AC1 23 TRP A 414 VAL A 415 ASP A 417 TYR A 483 SITE 4 AC1 23 THR A 484 ASN A 485 HOH A 528 HOH A 535 SITE 5 AC1 23 HOH A 556 HOH A 559 HOH A 602 HOH A 624 SITE 6 AC1 23 HOH A 651 HOH A 681 HOH A 798 SITE 1 AC2 5 HIS A 142 GLN A 450 GLU A 454 ASP A 463 SITE 2 AC2 5 HOH A 694 SITE 1 AC3 3 HIS A 208 GLU A 473 HOH A 752 SITE 1 AC4 5 LYS A 279 HIS A 314 ASP A 318 HOH A 649 SITE 2 AC4 5 HOH A 654 SITE 1 AC5 4 HIS A 515 HOH A 521 HOH A 795 HOH A 858 CRYST1 165.074 165.074 38.167 90.00 90.00 120.00 P 6 6 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 0.006058 0.003498 0.000000 0.00000 SCALE2 0.000000 0.006995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026201 0.00000