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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: 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