HEADER PEPTIDE BINDING PROTEIN 11-JUL-08 3DRK TITLE CRYSTAL STRUCTURE OF LACTOCOCCAL OPPA CO-CRYSTALLIZED WITH TITLE 2 NEUROPEPTIDE S IN AN OPEN CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGOPEPTIDE-BINDING PROTEIN OPPA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEUROPEPTIDE S; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; SOURCE 3 ORGANISM_TAXID: 416870; SOURCE 4 STRAIN: SUBSP. CREMORIS MG1363; SOURCE 5 GENE: OPPA, LLMG_0701; SOURCE 6 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1358; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MG1363; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAMP21; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIS KEYWDS OLIGO-PEPTIDE BINDING, VOLUMINOUS BINDING CAVITY, VENUS FLY-TRAP, KEYWDS 2 PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.P.-A.BERNTSSON,M.K.DOEVEN,R.H.DUURKENS,D.SENGUPTA,S.-J.MARRINK,A.- AUTHOR 2 M.THUNNISSEN,B.POOLMAN,D.-J.SLOTBOOM REVDAT 4 01-NOV-23 3DRK 1 SEQADV REVDAT 3 05-FEB-14 3DRK 1 JRNL REVDAT 2 13-JUL-11 3DRK 1 VERSN REVDAT 1 31-MAR-09 3DRK 0 JRNL AUTH R.P.-A.BERNTSSON,M.K.DOEVEN,F.FUSETTI,R.H.DUURKENS, JRNL AUTH 2 D.SENGUPTA,S.-J.MARRINK,A.-M.THUNNISSEN,B.POOLMAN, JRNL AUTH 3 D.-J.SLOTBOOM JRNL TITL THE STRUCTURAL BASIS FOR PEPTIDE SELECTION BY THE TRANSPORT JRNL TITL 2 RECEPTOR OPPA JRNL REF EMBO J. V. 28 1332 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19300437 JRNL DOI 10.1038/EMBOJ.2009.65 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 47251 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2518 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3420 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4387 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : 0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.728 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4513 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3031 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6116 ; 1.238 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7447 ; 0.852 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 568 ; 6.488 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;38.894 ;25.729 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 769 ;13.948 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;24.748 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5066 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 869 ; 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): 2817 ; 0.580 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1151 ; 0.144 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4532 ; 1.031 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1696 ; 1.665 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1584 ; 2.585 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 14 A 299 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8581 3.9337 -4.8253 REMARK 3 T TENSOR REMARK 3 T11: -0.0193 T22: 0.0055 REMARK 3 T33: 0.0067 T12: 0.0092 REMARK 3 T13: 0.0028 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 0.5232 L22: 0.5072 REMARK 3 L33: 0.6056 L12: -0.1888 REMARK 3 L13: 0.1509 L23: -0.1766 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.1158 S13: -0.1078 REMARK 3 S21: 0.0401 S22: -0.0261 S23: 0.0478 REMARK 3 S31: -0.0379 S32: -0.0072 S33: -0.0183 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 300 A 470 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2763 32.3635 19.7053 REMARK 3 T TENSOR REMARK 3 T11: 0.0139 T22: 0.0096 REMARK 3 T33: -0.0013 T12: 0.0049 REMARK 3 T13: -0.0006 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.8155 L22: 0.5345 REMARK 3 L33: 0.6173 L12: -0.0010 REMARK 3 L13: 0.0656 L23: -0.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.0285 S12: -0.1331 S13: 0.0976 REMARK 3 S21: 0.0825 S22: 0.0527 S23: 0.0040 REMARK 3 S31: 0.0215 S32: -0.0287 S33: -0.0242 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 471 A 572 REMARK 3 ORIGIN FOR THE GROUP (A): 8.3709 21.6717 4.8486 REMARK 3 T TENSOR REMARK 3 T11: 0.0232 T22: 0.0108 REMARK 3 T33: 0.0121 T12: -0.0010 REMARK 3 T13: 0.0022 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.3303 L22: 0.8418 REMARK 3 L33: 0.0058 L12: -0.2229 REMARK 3 L13: 0.0032 L23: 0.0608 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: 0.0313 S13: 0.0309 REMARK 3 S21: -0.0140 S22: 0.0328 S23: -0.0021 REMARK 3 S31: 0.0278 S32: -0.0128 S33: -0.0305 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC Q210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54564 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 42.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3DRF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M NA-HEPES, 20% PEG REMARK 280 6000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 61.56300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 GLN A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 THR A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 LYS A 12 REMARK 465 LYS A 13 REMARK 465 ALA A 573 REMARK 465 LYS A 574 REMARK 465 LEU A 575 REMARK 465 ALA A 576 REMARK 465 THR A 577 REMARK 465 LYS A 578 REMARK 465 GLY A 579 REMARK 465 SER A 580 REMARK 465 ILE A 581 REMARK 465 GLU A 582 REMARK 465 GLY A 583 REMARK 465 ARG A 584 REMARK 465 HIS A 585 REMARK 465 HIS A 586 REMARK 465 HIS A 587 REMARK 465 HIS A 588 REMARK 465 HIS A 589 REMARK 465 HIS A 590 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 GLU A 94 CD GLU A 94 OE1 -0.080 REMARK 500 GLU A 94 CD GLU A 94 OE2 -0.075 REMARK 500 GLU A 256 CD GLU A 256 OE1 -0.072 REMARK 500 TYR A 272 CD1 TYR A 272 CE1 -0.098 REMARK 500 SER A 571 CB SER A 571 OG -0.079 REMARK 500 PHE B 2 CD1 PHE B 2 CE1 -0.120 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 LEU A 14 CA - CB - CG ANGL. DEV. = 17.3 DEGREES REMARK 500 SER A 398 C - N - CA ANGL. DEV. = -17.3 DEGREES REMARK 500 ARG A 416 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ASP A 76 -167.86 -78.71 REMARK 500 ASP A 76 -168.78 -78.71 REMARK 500 THR A 215 -71.57 -124.95 REMARK 500 GLU A 233 -57.77 -125.23 REMARK 500 THR A 325 144.28 -172.75 REMARK 500 ASN A 341 59.85 -113.16 REMARK 500 ASN A 396 50.13 -100.07 REMARK 500 LYS A 397 -55.21 7.92 REMARK 500 ALA A 420 -39.48 -31.50 REMARK 500 THR A 539 -73.56 -105.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 396 12.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DRF RELATED DB: PDB REMARK 900 RELATED ID: 3DRG RELATED DB: PDB REMARK 900 RELATED ID: 3DRH RELATED DB: PDB REMARK 900 RELATED ID: 3DRI RELATED DB: PDB REMARK 900 RELATED ID: 3DRJ RELATED DB: PDB DBREF 3DRK A 2 578 UNP A2RJ53 A2RJ53_LACLM 24 600 DBREF 3DRK B 1 5 PDB 3DRK 3DRK 1 5 SEQADV 3DRK MET A 1 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK GLY A 579 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK SER A 580 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK ILE A 581 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK GLU A 582 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK GLY A 583 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK ARG A 584 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 585 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 586 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 587 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 588 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 589 UNP A2RJ53 EXPRESSION TAG SEQADV 3DRK HIS A 590 UNP A2RJ53 EXPRESSION TAG SEQRES 1 A 590 MET GLY SER ASN GLN SER SER SER THR SER THR LYS LYS SEQRES 2 A 590 LEU LYS ALA GLY ASN PHE ASP VAL ALA TYR GLN ASN PRO SEQRES 3 A 590 ASP LYS ALA ILE LYS GLY GLY ASN LEU LYS VAL ALA TYR SEQRES 4 A 590 GLN SER ASP SER PRO MET LYS ALA GLN TRP LEU SER GLY SEQRES 5 A 590 LEU SER ASN ASP ALA THR PHE ALA THR MET SER GLY PRO SEQRES 6 A 590 GLY GLY GLY GLN ASP GLY LEU PHE PHE THR ASP SER GLY SEQRES 7 A 590 PHE LYS PHE ILE LYS GLY GLY ALA ALA ASP VAL ALA LEU SEQRES 8 A 590 ASP LYS GLU SER LYS THR ALA THR ILE THR LEU ARG LYS SEQRES 9 A 590 ASP LEU LYS TRP SER ASP GLY SER GLU VAL THR ALA LYS SEQRES 10 A 590 ASP TYR GLU PHE THR TYR GLU THR ILE ALA ASN PRO ALA SEQRES 11 A 590 TYR GLY SER ASP ARG TRP THR ASP SER LEU ALA ASN ILE SEQRES 12 A 590 VAL GLY LEU SER ASP TYR HIS THR GLY LYS ALA LYS THR SEQRES 13 A 590 ILE SER GLY ILE THR PHE PRO ASP GLY GLU ASN GLY LYS SEQRES 14 A 590 VAL ILE LYS VAL GLN PHE LYS GLU MET LYS PRO GLY MET SEQRES 15 A 590 THR GLN SER GLY ASN GLY TYR PHE LEU GLU THR VAL ALA SEQRES 16 A 590 PRO TYR GLN TYR LEU LYS ASP VAL ALA PRO LYS ASP LEU SEQRES 17 A 590 ALA SER SER PRO LYS THR THR THR LYS PRO LEU VAL THR SEQRES 18 A 590 GLY PRO PHE LYS PRO GLU ASN VAL VAL ALA GLY GLU SER SEQRES 19 A 590 ILE LYS TYR VAL PRO ASN PRO TYR TYR TRP GLY GLU LYS SEQRES 20 A 590 PRO LYS LEU ASN SER ILE THR TYR GLU VAL VAL SER THR SEQRES 21 A 590 ALA LYS SER VAL ALA ALA LEU SER SER SER LYS TYR ASP SEQRES 22 A 590 ILE ILE ASN GLY MET VAL SER SER GLN TYR LYS GLN VAL SEQRES 23 A 590 LYS ASN LEU LYS GLY TYR LYS VAL LEU GLY GLN GLN ALA SEQRES 24 A 590 MET TYR ILE SER LEU MET TYR TYR ASN LEU GLY HIS TYR SEQRES 25 A 590 ASP ALA LYS ASN SER ILE ASN VAL GLN ASP ARG LYS THR SEQRES 26 A 590 PRO LEU GLN ASP GLN ASN VAL ARG GLN ALA ILE GLY TYR SEQRES 27 A 590 ALA ARG ASN VAL ALA GLU VAL ASP ASN LYS PHE SER ASN SEQRES 28 A 590 GLY LEU SER THR PRO ALA ASN SER LEU ILE PRO PRO ILE SEQRES 29 A 590 PHE LYS GLN PHE THR SER SER SER VAL LYS GLY TYR GLU SEQRES 30 A 590 LYS GLN ASP LEU ASP LYS ALA ASN LYS LEU LEU ASP GLU SEQRES 31 A 590 ASP GLY TRP LYS LEU ASN LYS SER THR GLY TYR ARG GLU SEQRES 32 A 590 LYS ASP GLY LYS GLU LEU SER LEU VAL TYR ALA ALA ARG SEQRES 33 A 590 VAL GLY ASP ALA ASN ALA GLU THR ILE ALA GLN ASN TYR SEQRES 34 A 590 ILE GLN GLN TRP LYS LYS ILE GLY VAL LYS VAL SER LEU SEQRES 35 A 590 TYR ASN GLY LYS LEU MET GLU PHE ASN SER TRP VAL ASP SEQRES 36 A 590 HIS MET THR THR PRO PRO GLY ALA ASN ASP TRP ASP ILE SEQRES 37 A 590 THR ASP GLY SER TRP SER LEU ALA SER GLU PRO SER GLN SEQRES 38 A 590 GLN ASP LEU PHE SER ALA ALA ALA PRO TYR ASN PHE GLY SEQRES 39 A 590 HIS PHE ASN ASP SER GLU ILE THR LYS ASP LEU ASN ASP SEQRES 40 A 590 ILE ASP SER ALA LYS SER GLU ASN PRO THR TYR ARG LYS SEQRES 41 A 590 ALA ALA PHE VAL LYS TYR GLN GLU ASP MET ASN LYS LYS SEQRES 42 A 590 ALA TYR VAL ILE PRO THR ASN PHE MET LEU ASN TYR THR SEQRES 43 A 590 PRO VAL ASN LYS ARG VAL VAL GLY MET THR LEU ASP TYR SEQRES 44 A 590 GLY ALA MET ASN THR TRP SER GLU ILE GLY VAL SER SER SEQRES 45 A 590 ALA LYS LEU ALA THR LYS GLY SER ILE GLU GLY ARG HIS SEQRES 46 A 590 HIS HIS HIS HIS HIS SEQRES 1 B 5 SER PHE ALA ASN GLY FORMUL 3 HOH *497(H2 O) HELIX 1 1 LEU A 50 SER A 54 5 5 HELIX 2 2 ASP A 56 SER A 63 1 8 HELIX 3 3 GLY A 64 GLY A 67 5 4 HELIX 4 4 THR A 115 ASN A 128 1 14 HELIX 5 5 PRO A 129 GLY A 132 5 4 HELIX 6 6 THR A 137 ILE A 143 5 7 HELIX 7 7 GLY A 145 THR A 151 1 7 HELIX 8 8 LYS A 179 GLN A 184 5 6 HELIX 9 9 PRO A 196 LYS A 201 1 6 HELIX 10 10 ALA A 204 THR A 215 5 12 HELIX 11 11 SER A 259 SER A 269 1 11 HELIX 12 12 VAL A 279 SER A 281 5 3 HELIX 13 13 GLN A 282 ASN A 288 1 7 HELIX 14 14 THR A 325 GLN A 328 5 4 HELIX 15 15 ASP A 329 ARG A 340 1 12 HELIX 16 16 ASN A 341 SER A 350 1 10 HELIX 17 17 ASP A 380 GLU A 390 1 11 HELIX 18 18 ASN A 421 ILE A 436 1 16 HELIX 19 19 ASN A 444 LYS A 446 5 3 HELIX 20 20 GLU A 449 THR A 459 1 11 HELIX 21 21 GLN A 481 SER A 486 1 6 HELIX 22 22 ASP A 498 ASP A 509 1 12 HELIX 23 23 SER A 510 GLU A 514 5 5 HELIX 24 24 ASN A 515 ALA A 534 1 20 HELIX 25 25 ASN A 563 ILE A 568 1 6 SHEET 1 A 2 LYS A 15 ALA A 16 0 SHEET 2 A 2 PHE A 19 ASP A 20 -1 O PHE A 19 N ALA A 16 SHEET 1 B 5 PHE A 224 VAL A 230 0 SHEET 2 B 5 SER A 234 PRO A 239 -1 O LYS A 236 N GLU A 227 SHEET 3 B 5 SER A 252 VAL A 258 -1 O ILE A 253 N TYR A 237 SHEET 4 B 5 ASN A 34 GLN A 40 1 N VAL A 37 O THR A 254 SHEET 5 B 5 ILE A 274 ASN A 276 1 O ASN A 276 N GLN A 40 SHEET 1 C 4 ALA A 87 ASP A 92 0 SHEET 2 C 4 THR A 97 LEU A 102 -1 O THR A 101 N ASP A 88 SHEET 3 C 4 VAL A 170 GLN A 174 -1 O VAL A 173 N ALA A 98 SHEET 4 C 4 ILE A 160 THR A 161 -1 N THR A 161 O LYS A 172 SHEET 1 D 6 TYR A 292 GLN A 298 0 SHEET 2 D 6 VAL A 536 ASN A 549 -1 O VAL A 548 N LYS A 293 SHEET 3 D 6 TYR A 301 TYR A 307 -1 N SER A 303 O THR A 539 SHEET 4 D 6 ILE A 468 SER A 474 -1 O GLY A 471 N LEU A 304 SHEET 5 D 6 SER A 410 ALA A 414 1 N ALA A 414 O ILE A 468 SHEET 6 D 6 LYS A 439 LEU A 442 1 O LYS A 439 N LEU A 411 SHEET 1 E 5 SER A 354 PRO A 356 0 SHEET 2 E 5 VAL A 536 ASN A 549 -1 O PHE A 541 N THR A 355 SHEET 3 E 5 TYR A 301 TYR A 307 -1 N SER A 303 O THR A 539 SHEET 4 E 5 ILE A 468 SER A 474 -1 O GLY A 471 N LEU A 304 SHEET 5 E 5 ALA B 3 ASN B 4 -1 O ALA B 3 N SER A 474 SHEET 1 F 2 HIS A 311 ASP A 313 0 SHEET 2 F 2 ILE A 318 VAL A 320 -1 O ILE A 318 N ASP A 313 SHEET 1 G 3 LYS A 394 LEU A 395 0 SHEET 2 G 3 ARG A 402 LYS A 404 -1 O GLU A 403 N LYS A 394 SHEET 3 G 3 LYS A 407 GLU A 408 -1 O LYS A 407 N LYS A 404 SHEET 1 H 2 VAL A 552 VAL A 553 0 SHEET 2 H 2 GLY A 569 VAL A 570 -1 O GLY A 569 N VAL A 553 CISPEP 1 PRO A 460 PRO A 461 0 7.52 CRYST1 39.622 123.126 59.281 90.00 102.31 90.00 P 1 21 1 2 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 0.025238 0.000000 0.005508 0.00000 SCALE2 0.000000 0.008122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017266 0.00000