HEADER CHAPERONE, PEPTIDE BINDING PROTEIN 13-NOV-12 4HY9
TITLE CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E.COLI DNAK IN
TITLE 2 COMPLEX WITH PYRRHOCORICIN_LYZZ (RESIDUES 1 TO 11)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CHAPERONE PROTEIN DNAK;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 389-607;
COMPND 5 SYNONYM: HSP70, HEAT SHOCK 70 KDA PROTEIN, HEAT SHOCK PROTEIN 70;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: PYRRHOCORICIN;
COMPND 9 CHAIN: C, D;
COMPND 10 FRAGMENT: UNP RESIDUES 1-11;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 83333;
SOURCE 4 STRAIN: K12;
SOURCE 5 GENE: DNAK, GROP, GRPF, SEG, B0014, JW0013;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: PYRRHOCORIS APTERUS;
SOURCE 11 ORGANISM_TAXID: 37000;
SOURCE 12 OTHER_DETAILS: PYRRHOCORICIN OCCURS NATURALLY IN PYRRHOCORIS
SOURCE 13 APTERUS.
KEYWDS CHAPERONE, ANTIMICROBIAL PEPTIDES, PEPTIDE BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR M.ZAHN,N.STRAETER
REVDAT 3 15-NOV-17 4HY9 1 REMARK
REVDAT 2 17-JUL-13 4HY9 1 JRNL
REVDAT 1 17-APR-13 4HY9 0
JRNL AUTH M.ZAHN,N.BERTHOLD,B.KIESLICH,D.KNAPPE,R.HOFFMANN,N.STRATER
JRNL TITL STRUCTURAL STUDIES ON THE FORWARD AND REVERSE BINDING MODES
JRNL TITL 2 OF PEPTIDES TO THE CHAPERONE DNAK.
JRNL REF J.MOL.BIOL. V. 425 2463 2013
JRNL REFN ISSN 0022-2836
JRNL PMID 23562829
JRNL DOI 10.1016/J.JMB.2013.03.041
REMARK 2
REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.60
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 80303
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) : 0.212
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1624
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) : 1.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5870
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.2940
REMARK 3 BIN FREE R VALUE SET COUNT : 109
REMARK 3 BIN FREE R VALUE : 0.3790
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3400
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 20
REMARK 3 SOLVENT ATOMS : 386
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.60000
REMARK 3 B22 (A**2) : -0.76000
REMARK 3 B33 (A**2) : 2.36000
REMARK 3 B12 (A**2) : 0.00000
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): 0.081
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.024
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3501 ; 0.022 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4736 ; 2.340 ; 1.992
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 456 ; 5.453 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;39.052 ;26.581
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 661 ;15.517 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.253 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 562 ; 0.199 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2558 ; 0.013 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 389 A 516
REMARK 3 ORIGIN FOR THE GROUP (A): -30.8459 36.5216 -22.0234
REMARK 3 T TENSOR
REMARK 3 T11: 0.0949 T22: 0.0988
REMARK 3 T33: 0.0046 T12: 0.0015
REMARK 3 T13: -0.0016 T23: -0.0077
REMARK 3 L TENSOR
REMARK 3 L11: 0.8411 L22: 0.2377
REMARK 3 L33: 0.0783 L12: -0.0843
REMARK 3 L13: -0.2173 L23: -0.0461
REMARK 3 S TENSOR
REMARK 3 S11: -0.0127 S12: -0.0048 S13: 0.0587
REMARK 3 S21: 0.0049 S22: 0.0265 S23: -0.0082
REMARK 3 S31: 0.0129 S32: -0.0156 S33: -0.0138
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 517 A 551
REMARK 3 ORIGIN FOR THE GROUP (A): -40.6899 20.8979 -13.0474
REMARK 3 T TENSOR
REMARK 3 T11: 0.0925 T22: 0.0854
REMARK 3 T33: 0.0415 T12: -0.0088
REMARK 3 T13: 0.0120 T23: 0.0421
REMARK 3 L TENSOR
REMARK 3 L11: 8.2017 L22: 0.3444
REMARK 3 L33: 2.1690 L12: -0.2263
REMARK 3 L13: -4.0131 L23: -0.0063
REMARK 3 S TENSOR
REMARK 3 S11: 0.0853 S12: 0.0888 S13: 0.0820
REMARK 3 S21: -0.0171 S22: 0.0455 S23: 0.0433
REMARK 3 S31: -0.0788 S32: -0.1400 S33: -0.1308
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 552 A 601
REMARK 3 ORIGIN FOR THE GROUP (A): -54.5752 17.2702 -2.7931
REMARK 3 T TENSOR
REMARK 3 T11: 0.0695 T22: 0.1679
REMARK 3 T33: 0.0545 T12: -0.0072
REMARK 3 T13: 0.0134 T23: 0.0725
REMARK 3 L TENSOR
REMARK 3 L11: 5.4338 L22: 1.4309
REMARK 3 L33: 2.3360 L12: -0.4848
REMARK 3 L13: -2.0586 L23: -0.6941
REMARK 3 S TENSOR
REMARK 3 S11: -0.0422 S12: -0.1579 S13: 0.0532
REMARK 3 S21: 0.1556 S22: 0.2393 S23: 0.2333
REMARK 3 S31: -0.1067 S32: -0.3203 S33: -0.1971
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 389 B 508
REMARK 3 ORIGIN FOR THE GROUP (A): -11.3100 19.1820 -5.8113
REMARK 3 T TENSOR
REMARK 3 T11: 0.0951 T22: 0.0750
REMARK 3 T33: 0.0407 T12: -0.0008
REMARK 3 T13: -0.0052 T23: 0.0079
REMARK 3 L TENSOR
REMARK 3 L11: 0.3775 L22: 0.7691
REMARK 3 L33: 0.4468 L12: -0.1789
REMARK 3 L13: -0.2500 L23: 0.3944
REMARK 3 S TENSOR
REMARK 3 S11: 0.0135 S12: -0.0680 S13: -0.0609
REMARK 3 S21: -0.0248 S22: 0.0154 S23: -0.1108
REMARK 3 S31: -0.0062 S32: 0.0193 S33: -0.0289
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 509 B 549
REMARK 3 ORIGIN FOR THE GROUP (A): -24.9143 9.5077 -6.6187
REMARK 3 T TENSOR
REMARK 3 T11: 0.0932 T22: 0.0730
REMARK 3 T33: 0.0495 T12: -0.0298
REMARK 3 T13: 0.0033 T23: 0.0161
REMARK 3 L TENSOR
REMARK 3 L11: 0.8086 L22: 1.8163
REMARK 3 L33: 0.2789 L12: -0.6039
REMARK 3 L13: -0.2332 L23: 0.4939
REMARK 3 S TENSOR
REMARK 3 S11: -0.1098 S12: 0.0319 S13: -0.1544
REMARK 3 S21: 0.0127 S22: 0.0984 S23: 0.1465
REMARK 3 S31: 0.0039 S32: -0.0475 S33: 0.0113
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 550 B 603
REMARK 3 ORIGIN FOR THE GROUP (A): -21.1876 -9.9842 -21.0321
REMARK 3 T TENSOR
REMARK 3 T11: 0.1637 T22: 0.2859
REMARK 3 T33: 0.0675 T12: -0.1296
REMARK 3 T13: 0.0119 T23: -0.1040
REMARK 3 L TENSOR
REMARK 3 L11: 2.9798 L22: 2.0672
REMARK 3 L33: 2.5122 L12: -0.1829
REMARK 3 L13: -0.6285 L23: 1.0515
REMARK 3 S TENSOR
REMARK 3 S11: -0.2364 S12: 0.7013 S13: -0.2935
REMARK 3 S21: -0.2294 S22: 0.1965 S23: 0.1415
REMARK 3 S31: 0.0180 S32: 0.1004 S33: 0.0398
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 4HY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-12.
REMARK 100 THE DEPOSITION ID IS D_1000076070.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-JUL-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.1
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.99188
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83099
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550
REMARK 200 RESOLUTION RANGE LOW (A) : 24.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
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: PDB ENTRY 3DPO
REMARK 200 SOFTWARE USED: REFINED WITH PDB CODE 3DPO
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.15
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, 0.1 M CITRIC
REMARK 280 ACID PH 4.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
REMARK 290 4555 X+1/2,-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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 38.70100
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 81.06550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.70100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 81.06550
REMARK 290 SMTRY3 4 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1290 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12520 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1270 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12230 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D
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 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 SD MET B 469 LIES ON A SPECIAL POSITION.
REMARK 400
REMARK 400 COMPOUND
REMARK 400
REMARK 400 THE PYRRHOCORICIN IS POLYPEPTIDE, A MEMBER OF ANTIMICROBIAL CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: PYRRHOCORICIN
REMARK 400 CHAIN: C, D
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
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 ALA A 602
REMARK 465 GLN A 603
REMARK 465 GLN A 604
REMARK 465 GLN A 605
REMARK 465 HIS A 606
REMARK 465 ALA A 607
REMARK 465 GLN B 604
REMARK 465 GLN B 605
REMARK 465 HIS B 606
REMARK 465 ALA B 607
REMARK 465 VAL C 1
REMARK 465 ASP C 2
REMARK 465 LYS C 3
REMARK 465 VAL D 1
REMARK 465 ASP D 2
REMARK 465 LYS D 3
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 THR C 12 CA C O CB OG1 CG2
REMARK 470 THR D 12 CA C O CB OG1 CG2
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 491 CD - CE - NZ ANGL. DEV. = -14.2 DEGREES
REMARK 500 LEU A 532 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES
REMARK 500 ILE B 418 CG1 - CB - CG2 ANGL. DEV. = 13.5 DEGREES
REMARK 500 ARG B 467 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
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 SO4 A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF PYRRHOCORICIN
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF PYRRHOCORICIN
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DKX RELATED DB: PDB
REMARK 900 RELATED ID: 1DKY RELATED DB: PDB
REMARK 900 RELATED ID: 1DKZ RELATED DB: PDB
REMARK 900 RELATED ID: 3DPO RELATED DB: PDB
REMARK 900 RELATED ID: 3DPP RELATED DB: PDB
REMARK 900 RELATED ID: 3DPQ RELATED DB: PDB
REMARK 900 RELATED ID: 3QNJ RELATED DB: PDB
REMARK 900 RELATED ID: 4E81 RELATED DB: PDB
REMARK 900 RELATED ID: 4HYB RELATED DB: PDB
DBREF 4HY9 A 389 607 UNP P0A6Y8 DNAK_ECOLI 389 607
DBREF 4HY9 B 389 607 UNP P0A6Y8 DNAK_ECOLI 389 607
DBREF 4HY9 C 1 11 UNP P37362 PYRRH_PYRAP 1 11
DBREF 4HY9 D 1 11 UNP P37362 PYRRH_PYRAP 1 11
SEQADV 4HY9 LEU C 4 UNP P37362 GLY 4 ENGINEERED MUTATION
SEQADV 4HY9 TYR C 5 UNP P37362 SER 5 ENGINEERED MUTATION
SEQADV 4HY9 ALC C 6 UNP P37362 TYR 6 ENGINEERED MUTATION
SEQADV 4HY9 ALC C 7 UNP P37362 LEU 7 ENGINEERED MUTATION
SEQADV 4HY9 THR C 12 UNP P37362 EXPRESSION TAG
SEQADV 4HY9 LEU D 4 UNP P37362 GLY 4 ENGINEERED MUTATION
SEQADV 4HY9 TYR D 5 UNP P37362 SER 5 ENGINEERED MUTATION
SEQADV 4HY9 ALC D 6 UNP P37362 TYR 6 ENGINEERED MUTATION
SEQADV 4HY9 ALC D 7 UNP P37362 LEU 7 ENGINEERED MUTATION
SEQADV 4HY9 THR D 12 UNP P37362 EXPRESSION TAG
SEQRES 1 A 219 VAL LEU LEU LEU ASP VAL THR PRO LEU SER LEU GLY ILE
SEQRES 2 A 219 GLU THR MET GLY GLY VAL MET THR THR LEU ILE ALA LYS
SEQRES 3 A 219 ASN THR THR ILE PRO THR LYS HIS SER GLN VAL PHE SER
SEQRES 4 A 219 THR ALA GLU ASP ASN GLN SER ALA VAL THR ILE HIS VAL
SEQRES 5 A 219 LEU GLN GLY GLU ARG LYS ARG ALA ALA ASP ASN LYS SER
SEQRES 6 A 219 LEU GLY GLN PHE ASN LEU ASP GLY ILE ASN PRO ALA PRO
SEQRES 7 A 219 ARG GLY MET PRO GLN ILE GLU VAL THR PHE ASP ILE ASP
SEQRES 8 A 219 ALA ASP GLY ILE LEU HIS VAL SER ALA LYS ASP LYS ASN
SEQRES 9 A 219 SER GLY LYS GLU GLN LYS ILE THR ILE LYS ALA SER SER
SEQRES 10 A 219 GLY LEU ASN GLU ASP GLU ILE GLN LYS MET VAL ARG ASP
SEQRES 11 A 219 ALA GLU ALA ASN ALA GLU ALA ASP ARG LYS PHE GLU GLU
SEQRES 12 A 219 LEU VAL GLN THR ARG ASN GLN GLY ASP HIS LEU LEU HIS
SEQRES 13 A 219 SER THR ARG LYS GLN VAL GLU GLU ALA GLY ASP LYS LEU
SEQRES 14 A 219 PRO ALA ASP ASP LYS THR ALA ILE GLU SER ALA LEU THR
SEQRES 15 A 219 ALA LEU GLU THR ALA LEU LYS GLY GLU ASP LYS ALA ALA
SEQRES 16 A 219 ILE GLU ALA LYS MET GLN GLU LEU ALA GLN VAL SER GLN
SEQRES 17 A 219 LYS LEU MET GLU ILE ALA GLN GLN GLN HIS ALA
SEQRES 1 B 219 VAL LEU LEU LEU ASP VAL THR PRO LEU SER LEU GLY ILE
SEQRES 2 B 219 GLU THR MET GLY GLY VAL MET THR THR LEU ILE ALA LYS
SEQRES 3 B 219 ASN THR THR ILE PRO THR LYS HIS SER GLN VAL PHE SER
SEQRES 4 B 219 THR ALA GLU ASP ASN GLN SER ALA VAL THR ILE HIS VAL
SEQRES 5 B 219 LEU GLN GLY GLU ARG LYS ARG ALA ALA ASP ASN LYS SER
SEQRES 6 B 219 LEU GLY GLN PHE ASN LEU ASP GLY ILE ASN PRO ALA PRO
SEQRES 7 B 219 ARG GLY MET PRO GLN ILE GLU VAL THR PHE ASP ILE ASP
SEQRES 8 B 219 ALA ASP GLY ILE LEU HIS VAL SER ALA LYS ASP LYS ASN
SEQRES 9 B 219 SER GLY LYS GLU GLN LYS ILE THR ILE LYS ALA SER SER
SEQRES 10 B 219 GLY LEU ASN GLU ASP GLU ILE GLN LYS MET VAL ARG ASP
SEQRES 11 B 219 ALA GLU ALA ASN ALA GLU ALA ASP ARG LYS PHE GLU GLU
SEQRES 12 B 219 LEU VAL GLN THR ARG ASN GLN GLY ASP HIS LEU LEU HIS
SEQRES 13 B 219 SER THR ARG LYS GLN VAL GLU GLU ALA GLY ASP LYS LEU
SEQRES 14 B 219 PRO ALA ASP ASP LYS THR ALA ILE GLU SER ALA LEU THR
SEQRES 15 B 219 ALA LEU GLU THR ALA LEU LYS GLY GLU ASP LYS ALA ALA
SEQRES 16 B 219 ILE GLU ALA LYS MET GLN GLU LEU ALA GLN VAL SER GLN
SEQRES 17 B 219 LYS LEU MET GLU ILE ALA GLN GLN GLN HIS ALA
SEQRES 1 C 12 VAL ASP LYS LEU TYR ALC ALC PRO ARG PRO THR THR
SEQRES 1 D 12 VAL ASP LYS LEU TYR ALC ALC PRO ARG PRO THR THR
MODRES 4HY9 ALC C 6 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
MODRES 4HY9 ALC C 7 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
MODRES 4HY9 ALC D 6 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
MODRES 4HY9 ALC D 7 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
HET ALC C 6 11
HET ALC C 7 11
HET ALC D 6 11
HET ALC D 7 11
HET SO4 A 701 5
HET SO4 B 701 5
HET SO4 B 702 5
HET SO4 C 101 5
HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
HETNAM SO4 SULFATE ION
FORMUL 3 ALC 4(C9 H17 N O2)
FORMUL 5 SO4 4(O4 S 2-)
FORMUL 9 HOH *386(H2 O)
HELIX 1 1 ARG A 447 ASN A 451 5 5
HELIX 2 2 ASN A 508 ASN A 522 1 15
HELIX 3 3 ASN A 522 GLY A 554 1 33
HELIX 4 4 ASP A 555 LEU A 557 5 3
HELIX 5 5 PRO A 558 LYS A 577 1 20
HELIX 6 6 ASP A 580 VAL A 594 1 15
HELIX 7 7 ARG B 447 ASN B 451 5 5
HELIX 8 8 ASN B 508 ASN B 522 1 15
HELIX 9 9 ASN B 522 GLY B 554 1 33
HELIX 10 10 ASP B 555 LEU B 557 5 3
HELIX 11 11 PRO B 558 GLY B 578 1 21
HELIX 12 12 ASP B 580 VAL B 594 1 15
HELIX 13 13 SER B 595 GLN B 603 1 9
SHEET 1 A 4 VAL A 407 ILE A 412 0
SHEET 2 A 4 LEU A 399 THR A 403 -1 N LEU A 399 O LEU A 411
SHEET 3 A 4 VAL A 436 GLN A 442 -1 O LEU A 441 N GLY A 400
SHEET 4 A 4 LYS A 452 LEU A 459 -1 O PHE A 457 N ILE A 438
SHEET 1 B 4 THR A 420 PHE A 426 0
SHEET 2 B 4 ILE A 472 ILE A 478 -1 O ILE A 478 N THR A 420
SHEET 3 B 4 LEU A 484 ASP A 490 -1 O HIS A 485 N ASP A 477
SHEET 4 B 4 GLU A 496 ILE A 501 -1 O ILE A 501 N LEU A 484
SHEET 1 C 4 VAL B 407 ILE B 412 0
SHEET 2 C 4 LEU B 399 THR B 403 -1 N ILE B 401 O THR B 409
SHEET 3 C 4 ALA B 435 GLN B 442 -1 O LEU B 441 N GLY B 400
SHEET 4 C 4 LYS B 452 ASP B 460 -1 O PHE B 457 N ILE B 438
SHEET 1 D 5 GLU B 496 ILE B 501 0
SHEET 2 D 5 LEU B 484 ASP B 490 -1 N LEU B 484 O ILE B 501
SHEET 3 D 5 ILE B 472 ILE B 478 -1 N ASP B 477 O HIS B 485
SHEET 4 D 5 THR B 420 THR B 428 -1 N PHE B 426 O ILE B 472
SHEET 5 D 5 ALC D 6 ALC D 7 1 O ALC D 7 N SER B 427
LINK C TYR C 5 N ALC C 6 1555 1555 1.32
LINK C ALC C 6 N ALC C 7 1555 1555 1.33
LINK C ALC C 7 N PRO C 8 1555 1555 1.34
LINK C TYR D 5 N ALC D 6 1555 1555 1.32
LINK C ALC D 6 N ALC D 7 1555 1555 1.35
LINK C ALC D 7 N PRO D 8 1555 1555 1.34
CISPEP 1 ILE A 418 PRO A 419 0 7.82
CISPEP 2 ILE B 418 PRO B 419 0 -2.17
SITE 1 AC1 4 ASN A 458 ASP A 460 HOH A 838 HOH A 967
SITE 1 AC2 4 ARG B 447 ARG B 536 GLU B 579 HOH B 939
SITE 1 AC3 4 LYS B 502 SER B 504 HOH B 814 HOH B 890
SITE 1 AC4 7 MET A 404 GLY A 405 PRO C 8 ARG C 9
SITE 2 AC4 7 HOH C 203 HOH C 207 HOH C 208
SITE 1 AC5 28 ILE A 401 GLU A 402 THR A 403 MET A 404
SITE 2 AC5 28 GLN A 424 VAL A 425 PHE A 426 SER A 427
SITE 3 AC5 28 THR A 428 GLU A 430 GLN A 433 VAL A 436
SITE 4 AC5 28 ARG A 467 ILE A 472 ASP A 540 HOH A 942
SITE 5 AC5 28 ASP B 510 THR C 12 SO4 C 101 HOH C 201
SITE 6 AC5 28 HOH C 202 HOH C 203 HOH C 204 HOH C 206
SITE 7 AC5 28 HOH C 209 HOH C 211 HOH C 213 HOH C 214
SITE 1 AC6 22 ARG A 517 ASP A 518 ILE B 401 GLU B 402
SITE 2 AC6 22 THR B 403 MET B 404 VAL B 425 PHE B 426
SITE 3 AC6 22 SER B 427 THR B 428 ALA B 429 GLN B 433
SITE 4 AC6 22 ALA B 435 VAL B 436 THR B 437 ILE B 438
SITE 5 AC6 22 GLY B 468 HOH B 807 HOH B 912 THR D 12
SITE 6 AC6 22 HOH D 101 HOH D 103
CRYST1 77.402 162.131 45.279 90.00 90.00 90.00 P 21 21 2 8
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 0.012920 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006168 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022085 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
