HEADER MEMBRANE PROTEIN/ANTIBIOTIC 30-JUL-12 4GCP TITLE CRYSTAL STRUCTURE OF E. COLI OMPF PORIN IN COMPLEX WITH AMPICILLIN CAVEAT 4GCP POOR COVALENT BOND ANGLES FOR RESIDUES A46, A162, A209, B209 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN F; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 23-362; COMPND 5 SYNONYM: OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN B, OUTER COMPND 6 MEMBRANE PROTEIN IA, PORIN OMPF; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: OMPF, CMLB, COA, CRY, TOLF, B0929, JW0912; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-BARREL, PROTEIN-DRUG COMPLEX, TRIMER, NON-SPECIFIC CHANNEL, KEYWDS 2 AMPICILLIN BINDING, OUTER MEMBRANE, MEMBRANE PROTEIN-ANTIBIOTIC KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.K.ZIERVOGEL,B.ROUX REVDAT 3 28-FEB-24 4GCP 1 REMARK SEQADV REVDAT 2 06-FEB-13 4GCP 1 JRNL REVDAT 1 19-DEC-12 4GCP 0 JRNL AUTH B.K.ZIERVOGEL,B.ROUX JRNL TITL THE BINDING OF ANTIBIOTICS IN OMPF PORIN. JRNL REF STRUCTURE V. 21 76 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23201272 JRNL DOI 10.1016/J.STR.2012.10.014 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 52782 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2836 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3845 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 211 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5136 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.84000 REMARK 3 B22 (A**2) : -2.84000 REMARK 3 B33 (A**2) : 4.26000 REMARK 3 B12 (A**2) : -1.42000 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): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.734 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5262 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7148 ; 2.060 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 668 ; 6.979 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 280 ;37.318 ;24.786 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 730 ;14.879 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.196 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 734 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4266 ; 0.009 ; 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): 3254 ; 1.135 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5128 ; 1.942 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2008 ; 2.916 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2016 ; 4.309 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 340 1 REMARK 3 1 B 8 B 340 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 2548 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 2548 ; 0.16 ; 0.50 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GCP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55640 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER V2.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 200, 0.1 M SODIUM CACODYLATE, REMARK 280 0.2 M MAGNESIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 58.30000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -100.97856 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 116.60000 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 116.60000 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 58.30000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 100.97856 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 620 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 617 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 ILE A 3 REMARK 465 TYR A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 GLY B 0 REMARK 465 ALA B 1 REMARK 465 GLU B 2 REMARK 465 ILE B 3 REMARK 465 TYR B 4 REMARK 465 ASN B 5 REMARK 465 LYS B 6 REMARK 465 ASP B 7 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 LYS A 10 CG CD CE NZ REMARK 480 GLU A 29 CG CD OE1 OE2 REMARK 480 LYS A 46 CE NZ REMARK 480 GLU A 162 CD OE1 OE2 REMARK 480 GLU A 183 CG CD OE1 OE2 REMARK 480 LYS A 209 CD CE NZ REMARK 480 LYS A 210 CD CE NZ REMARK 480 LYS A 243 CG CD CE NZ REMARK 480 LYS A 323 CG CD CE NZ REMARK 480 LYS B 10 CG CD CE NZ REMARK 480 GLU B 29 CG CD OE1 OE2 REMARK 480 LYS B 46 CE NZ REMARK 480 GLU B 162 CD OE1 OE2 REMARK 480 GLU B 183 CG CD OE1 OE2 REMARK 480 LYS B 209 CD CE NZ REMARK 480 LYS B 210 CD CE NZ REMARK 480 LYS B 243 CG CD CE NZ REMARK 480 LYS B 323 CG CD CE NZ 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 ASN B 207 O HOH B 627 1.99 REMARK 500 OD1 ASN B 246 O HOH B 540 2.08 REMARK 500 SD MET B 38 O HOH B 621 2.15 REMARK 500 OG SER B 179 O HOH B 573 2.16 REMARK 500 O ASN A 207 O HOH A 628 2.16 REMARK 500 SD MET A 38 O HOH A 579 2.17 REMARK 500 O HOH A 555 O HOH A 568 2.18 REMARK 500 O HOH A 622 O HOH A 632 2.18 REMARK 500 OE2 GLU B 212 O HOH B 563 2.19 REMARK 500 OD1 ASP A 266 O HOH A 616 2.19 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 LYS A 46 CD LYS A 46 CE -0.415 REMARK 500 GLU A 162 CG GLU A 162 CD -0.300 REMARK 500 SER A 177 CB SER A 177 OG 0.088 REMARK 500 GLU A 183 CB GLU A 183 CG -0.237 REMARK 500 TYR A 301 CD1 TYR A 301 CE1 0.090 REMARK 500 LYS B 46 CD LYS B 46 CE -0.154 REMARK 500 GLU B 162 CG GLU B 162 CD -0.235 REMARK 500 GLU B 183 CB GLU B 183 CG -0.324 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 LYS A 46 CG - CD - CE ANGL. DEV. = 29.0 DEGREES REMARK 500 GLU A 162 CG - CD - OE1 ANGL. DEV. = -39.5 DEGREES REMARK 500 GLU A 162 CG - CD - OE2 ANGL. DEV. = 32.0 DEGREES REMARK 500 LYS A 209 CB - CG - CD ANGL. DEV. = 31.5 DEGREES REMARK 500 LYS B 209 CB - CG - CD ANGL. DEV. = 34.9 DEGREES REMARK 500 LYS B 210 CG - CD - CE ANGL. DEV. = 18.7 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 ALA A 84 101.32 -161.47 REMARK 500 ALA A 91 -106.16 29.37 REMARK 500 GLU A 117 -43.85 -132.37 REMARK 500 PHE A 118 -137.51 -98.26 REMARK 500 PHE A 128 -111.06 59.40 REMARK 500 PHE A 144 73.11 35.89 REMARK 500 GLU A 183 60.65 39.65 REMARK 500 ASP A 221 75.52 -154.55 REMARK 500 ILE A 286 -38.84 -141.40 REMARK 500 ASN A 293 104.30 -168.75 REMARK 500 ASN A 304 -167.87 -169.47 REMARK 500 ALA B 84 100.10 -160.60 REMARK 500 ALA B 91 -107.12 28.47 REMARK 500 GLU B 117 -42.80 -135.09 REMARK 500 PHE B 118 -140.29 -96.42 REMARK 500 PHE B 128 -113.77 54.78 REMARK 500 PHE B 144 74.61 38.81 REMARK 500 GLU B 183 62.60 36.01 REMARK 500 ASP B 221 76.40 -154.12 REMARK 500 ILE B 286 -42.60 -139.65 REMARK 500 ASN B 293 104.87 -164.89 REMARK 500 ASN B 304 -168.03 -169.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 162 0.07 SIDE CHAIN 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 AIC A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AIC B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GCQ RELATED DB: PDB REMARK 900 E. COLI OMPF IN COMPLEX WITH CARBENICILLIN REMARK 900 RELATED ID: 4GCS RELATED DB: PDB REMARK 900 E. COLI OMPF IN COMPLEX WITH ERTAPENEM DBREF 4GCP A 1 340 UNP P02931 OMPF_ECOLI 23 362 DBREF 4GCP B 1 340 UNP P02931 OMPF_ECOLI 23 362 SEQADV 4GCP GLY A 0 UNP P02931 EXPRESSION TAG SEQADV 4GCP GLY B 0 UNP P02931 EXPRESSION TAG SEQRES 1 A 341 GLY ALA GLU ILE TYR ASN LYS ASP GLY ASN LYS VAL ASP SEQRES 2 A 341 LEU TYR GLY LYS ALA VAL GLY LEU HIS TYR PHE SER LYS SEQRES 3 A 341 GLY ASN GLY GLU ASN SER TYR GLY GLY ASN GLY ASP MET SEQRES 4 A 341 THR TYR ALA ARG LEU GLY PHE LYS GLY GLU THR GLN ILE SEQRES 5 A 341 ASN SER ASP LEU THR GLY TYR GLY GLN TRP GLU TYR ASN SEQRES 6 A 341 PHE GLN GLY ASN ASN SER GLU GLY ALA ASP ALA GLN THR SEQRES 7 A 341 GLY ASN LYS THR ARG LEU ALA PHE ALA GLY LEU LYS TYR SEQRES 8 A 341 ALA ASP VAL GLY SER PHE ASP TYR GLY ARG ASN TYR GLY SEQRES 9 A 341 VAL VAL TYR ASP ALA LEU GLY TYR THR ASP MET LEU PRO SEQRES 10 A 341 GLU PHE GLY GLY ASP THR ALA TYR SER ASP ASP PHE PHE SEQRES 11 A 341 VAL GLY ARG VAL GLY GLY VAL ALA THR TYR ARG ASN SER SEQRES 12 A 341 ASN PHE PHE GLY LEU VAL ASP GLY LEU ASN PHE ALA VAL SEQRES 13 A 341 GLN TYR LEU GLY LYS ASN GLU ARG ASP THR ALA ARG ARG SEQRES 14 A 341 SER ASN GLY ASP GLY VAL GLY GLY SER ILE SER TYR GLU SEQRES 15 A 341 TYR GLU GLY PHE GLY ILE VAL GLY ALA TYR GLY ALA ALA SEQRES 16 A 341 ASP ARG THR ASN LEU GLN GLU ALA GLN PRO LEU GLY ASN SEQRES 17 A 341 GLY LYS LYS ALA GLU GLN TRP ALA THR GLY LEU LYS TYR SEQRES 18 A 341 ASP ALA ASN ASN ILE TYR LEU ALA ALA ASN TYR GLY GLU SEQRES 19 A 341 THR ARG ASN ALA THR PRO ILE THR ASN LYS PHE THR ASN SEQRES 20 A 341 THR SER GLY PHE ALA ASN LYS THR GLN ASP VAL LEU LEU SEQRES 21 A 341 VAL ALA GLN TYR GLN PHE ASP PHE GLY LEU ARG PRO SER SEQRES 22 A 341 ILE ALA TYR THR LYS SER LYS ALA LYS ASP VAL GLU GLY SEQRES 23 A 341 ILE GLY ASP VAL ASP LEU VAL ASN TYR PHE GLU VAL GLY SEQRES 24 A 341 ALA THR TYR TYR PHE ASN LYS ASN MET SER THR TYR VAL SEQRES 25 A 341 ASP TYR ILE ILE ASN GLN ILE ASP SER ASP ASN LYS LEU SEQRES 26 A 341 GLY VAL GLY SER ASP ASP THR VAL ALA VAL GLY ILE VAL SEQRES 27 A 341 TYR GLN PHE SEQRES 1 B 341 GLY ALA GLU ILE TYR ASN LYS ASP GLY ASN LYS VAL ASP SEQRES 2 B 341 LEU TYR GLY LYS ALA VAL GLY LEU HIS TYR PHE SER LYS SEQRES 3 B 341 GLY ASN GLY GLU ASN SER TYR GLY GLY ASN GLY ASP MET SEQRES 4 B 341 THR TYR ALA ARG LEU GLY PHE LYS GLY GLU THR GLN ILE SEQRES 5 B 341 ASN SER ASP LEU THR GLY TYR GLY GLN TRP GLU TYR ASN SEQRES 6 B 341 PHE GLN GLY ASN ASN SER GLU GLY ALA ASP ALA GLN THR SEQRES 7 B 341 GLY ASN LYS THR ARG LEU ALA PHE ALA GLY LEU LYS TYR SEQRES 8 B 341 ALA ASP VAL GLY SER PHE ASP TYR GLY ARG ASN TYR GLY SEQRES 9 B 341 VAL VAL TYR ASP ALA LEU GLY TYR THR ASP MET LEU PRO SEQRES 10 B 341 GLU PHE GLY GLY ASP THR ALA TYR SER ASP ASP PHE PHE SEQRES 11 B 341 VAL GLY ARG VAL GLY GLY VAL ALA THR TYR ARG ASN SER SEQRES 12 B 341 ASN PHE PHE GLY LEU VAL ASP GLY LEU ASN PHE ALA VAL SEQRES 13 B 341 GLN TYR LEU GLY LYS ASN GLU ARG ASP THR ALA ARG ARG SEQRES 14 B 341 SER ASN GLY ASP GLY VAL GLY GLY SER ILE SER TYR GLU SEQRES 15 B 341 TYR GLU GLY PHE GLY ILE VAL GLY ALA TYR GLY ALA ALA SEQRES 16 B 341 ASP ARG THR ASN LEU GLN GLU ALA GLN PRO LEU GLY ASN SEQRES 17 B 341 GLY LYS LYS ALA GLU GLN TRP ALA THR GLY LEU LYS TYR SEQRES 18 B 341 ASP ALA ASN ASN ILE TYR LEU ALA ALA ASN TYR GLY GLU SEQRES 19 B 341 THR ARG ASN ALA THR PRO ILE THR ASN LYS PHE THR ASN SEQRES 20 B 341 THR SER GLY PHE ALA ASN LYS THR GLN ASP VAL LEU LEU SEQRES 21 B 341 VAL ALA GLN TYR GLN PHE ASP PHE GLY LEU ARG PRO SER SEQRES 22 B 341 ILE ALA TYR THR LYS SER LYS ALA LYS ASP VAL GLU GLY SEQRES 23 B 341 ILE GLY ASP VAL ASP LEU VAL ASN TYR PHE GLU VAL GLY SEQRES 24 B 341 ALA THR TYR TYR PHE ASN LYS ASN MET SER THR TYR VAL SEQRES 25 B 341 ASP TYR ILE ILE ASN GLN ILE ASP SER ASP ASN LYS LEU SEQRES 26 B 341 GLY VAL GLY SER ASP ASP THR VAL ALA VAL GLY ILE VAL SEQRES 27 B 341 TYR GLN PHE HET AIC A 401 24 HET AIC B 401 24 HETNAM AIC (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3, HETNAM 2 AIC 3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2- HETNAM 3 AIC CARBOXYLIC ACID HETSYN AIC AMPICILLIN; D(-)-ALPHA-AMINOBENZYLPENICILLIN; 6-[D(-)- HETSYN 2 AIC ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID FORMUL 3 AIC 2(C16 H19 N3 O4 S) FORMUL 5 HOH *263(H2 O) HELIX 1 1 VAL A 105 GLY A 110 1 6 HELIX 2 2 ASN A 143 LEU A 147 1 5 HELIX 3 3 THR A 165 SER A 169 5 5 HELIX 4 4 THR A 197 ALA A 202 1 6 HELIX 5 5 VAL B 105 GLY B 110 1 6 HELIX 6 6 SER B 142 LEU B 147 1 6 HELIX 7 7 THR B 197 ALA B 202 1 6 SHEET 1 A18 GLY A 36 ASP A 37 0 SHEET 2 A18 ASN A 9 PHE A 23 -1 N TYR A 22 O GLY A 36 SHEET 3 A18 THR A 331 PHE A 340 -1 O VAL A 332 N PHE A 23 SHEET 4 A18 MET A 307 ASN A 316 -1 N SER A 308 O VAL A 337 SHEET 5 A18 GLY A 287 TYR A 302 -1 N TYR A 301 O THR A 309 SHEET 6 A18 LEU A 269 VAL A 283 -1 N SER A 278 O LEU A 291 SHEET 7 A18 LYS A 253 TYR A 263 -1 N VAL A 257 O LYS A 277 SHEET 8 A18 ILE A 225 ARG A 235 -1 N GLY A 232 O ASP A 256 SHEET 9 A18 LYS A 210 ALA A 222 -1 N TRP A 214 O GLU A 233 SHEET 10 A18 PHE A 185 ASP A 195 -1 N VAL A 188 O GLY A 217 SHEET 11 A18 GLY A 173 TYR A 182 -1 N TYR A 180 O ILE A 187 SHEET 12 A18 LEU A 151 LEU A 158 -1 N ASN A 152 O SER A 179 SHEET 13 A18 ARG A 132 SER A 142 -1 N ALA A 137 O TYR A 157 SHEET 14 A18 GLY A 94 TYR A 102 -1 N ASN A 101 O VAL A 133 SHEET 15 A18 LYS A 80 TYR A 90 -1 N ALA A 84 O ARG A 100 SHEET 16 A18 LEU A 55 GLN A 66 -1 N ASN A 64 O LYS A 80 SHEET 17 A18 TYR A 40 ASN A 52 -1 N ALA A 41 O PHE A 65 SHEET 18 A18 ASN A 9 PHE A 23 -1 N VAL A 18 O TYR A 40 SHEET 1 B 2 PRO A 239 ASN A 242 0 SHEET 2 B 2 THR A 247 PHE A 250 -1 O THR A 247 N ASN A 242 SHEET 1 C18 GLY B 36 ASP B 37 0 SHEET 2 C18 ASN B 9 PHE B 23 -1 N TYR B 22 O GLY B 36 SHEET 3 C18 THR B 331 PHE B 340 -1 O VAL B 332 N PHE B 23 SHEET 4 C18 MET B 307 ASN B 316 -1 N ILE B 314 O THR B 331 SHEET 5 C18 GLY B 287 TYR B 302 -1 N TYR B 301 O THR B 309 SHEET 6 C18 LEU B 269 VAL B 283 -1 N SER B 278 O LEU B 291 SHEET 7 C18 LYS B 253 TYR B 263 -1 N VAL B 257 O LYS B 277 SHEET 8 C18 ILE B 225 ARG B 235 -1 N ASN B 230 O LEU B 258 SHEET 9 C18 LYS B 210 ALA B 222 -1 N TYR B 220 O LEU B 227 SHEET 10 C18 PHE B 185 ASP B 195 -1 N ALA B 194 O ALA B 211 SHEET 11 C18 GLY B 173 TYR B 182 -1 N TYR B 180 O ILE B 187 SHEET 12 C18 LEU B 151 LEU B 158 -1 N ASN B 152 O SER B 179 SHEET 13 C18 ARG B 132 ASN B 141 -1 N ALA B 137 O TYR B 157 SHEET 14 C18 GLY B 94 TYR B 102 -1 N SER B 95 O ARG B 140 SHEET 15 C18 LYS B 80 TYR B 90 -1 N ALA B 84 O ARG B 100 SHEET 16 C18 LEU B 55 GLN B 66 -1 N ASN B 64 O LYS B 80 SHEET 17 C18 TYR B 40 GLN B 50 -1 N LEU B 43 O TYR B 63 SHEET 18 C18 ASN B 9 PHE B 23 -1 N ASP B 12 O LYS B 46 SHEET 1 D 2 PRO B 239 ASN B 242 0 SHEET 2 D 2 THR B 247 PHE B 250 -1 O GLY B 249 N ILE B 240 CISPEP 1 ASN A 27 GLY A 28 0 -23.09 CISPEP 2 ASN B 27 GLY B 28 0 -21.88 SITE 1 AC1 10 TYR A 32 PHE A 118 GLY A 119 ASP A 121 SITE 2 AC1 10 TYR A 124 SER A 125 ARG A 167 HOH A 598 SITE 3 AC1 10 HOH A 617 HOH A 623 SITE 1 AC2 8 TYR B 32 PHE B 118 GLY B 119 ASP B 121 SITE 2 AC2 8 TYR B 124 SER B 125 ARG B 167 HOH B 596 CRYST1 116.600 116.600 53.270 90.00 90.00 120.00 P 3 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 0.008576 0.004952 0.000000 0.00000 SCALE2 0.000000 0.009903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018772 0.00000