HEADER CELL ADHESION 20-MAR-09 2WD6 TITLE CRYSTAL STRUCTURE OF THE VARIABLE DOMAIN OF THE STREPTOCOCCUS GORDONII TITLE 2 SURFACE PROTEIN SSPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VARIABLE DOMAIN, RESIDUES 449-797; COMPND 5 SYNONYM: SSP-5, CELL SURFACE ANTIGEN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS GORDONII; SOURCE 3 ORGANISM_TAXID: 1302; SOURCE 4 STRAIN: M5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-VECTOR KEYWDS CELL ADHESION, SECRETED, V-REGION, CELL WALL, AG I/II PROTEIN, KEYWDS 2 SURFACE ADHESIN, PEPTIDOGLYCAN-ANCHOR EXPDTA X-RAY DIFFRACTION AUTHOR N.FORSGREN,K.PERSSON REVDAT 5 08-MAY-24 2WD6 1 REMARK LINK REVDAT 4 17-JAN-18 2WD6 1 REMARK REVDAT 3 13-JUL-11 2WD6 1 VERSN REVDAT 2 24-NOV-09 2WD6 1 JRNL REVDAT 1 28-JUL-09 2WD6 0 JRNL AUTH N.FORSGREN,R.J.LAMONT,K.PERSSON JRNL TITL CRYSTAL STRUCTURE OF THE VARIABLE DOMAIN OF THE JRNL TITL 2 STREPTOCOCCUS GORDONII SURFACE PROTEIN SSPB. JRNL REF PROTEIN SCI. V. 18 1896 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19609934 JRNL DOI 10.1002/PRO.200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35258 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1853 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2606 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : -0.10000 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): 0.233 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.743 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4761 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6444 ; 1.634 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 593 ; 7.237 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;38.633 ;25.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 789 ;16.368 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.813 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3635 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2046 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3179 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 366 ; 0.156 ; 0.200 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): 22 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.110 ; 0.200 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): 2954 ; 0.668 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4758 ; 1.237 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1839 ; 2.363 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1686 ; 3.688 ; 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 : 2 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 462 A 762 REMARK 3 ORIGIN FOR THE GROUP (A): 41.7286 38.4478 75.5783 REMARK 3 T TENSOR REMARK 3 T11: -0.1521 T22: -0.1276 REMARK 3 T33: -0.0099 T12: 0.0226 REMARK 3 T13: -0.0121 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.5550 L22: 1.3868 REMARK 3 L33: 2.2578 L12: 0.1082 REMARK 3 L13: 0.1171 L23: -0.1263 REMARK 3 S TENSOR REMARK 3 S11: -0.0555 S12: -0.0492 S13: 0.1005 REMARK 3 S21: -0.0242 S22: 0.0207 S23: -0.2081 REMARK 3 S31: -0.0941 S32: 0.0610 S33: 0.0348 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 : B 467 B 760 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2499 41.3585 77.9319 REMARK 3 T TENSOR REMARK 3 T11: -0.1409 T22: 0.0636 REMARK 3 T33: -0.0371 T12: 0.0765 REMARK 3 T13: -0.0255 T23: -0.0401 REMARK 3 L TENSOR REMARK 3 L11: 3.6299 L22: 2.1974 REMARK 3 L33: 2.3527 L12: -0.6088 REMARK 3 L13: 0.8561 L23: 0.3127 REMARK 3 S TENSOR REMARK 3 S11: -0.1211 S12: -0.6430 S13: 0.1528 REMARK 3 S21: 0.0758 S22: 0.1561 S23: 0.1649 REMARK 3 S31: 0.0019 S32: -0.2262 S33: -0.0350 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2WD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91698 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37172 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 60.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.99 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.42 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KBR 25% PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 80.99333 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 40.49667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.74500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.24833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 101.24167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.1 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 GLU A 449 REMARK 465 ALA A 450 REMARK 465 LYS A 451 REMARK 465 LEU A 452 REMARK 465 ALA A 453 REMARK 465 LYS A 454 REMARK 465 TYR A 455 REMARK 465 GLU A 456 REMARK 465 ALA A 457 REMARK 465 ASP A 458 REMARK 465 LEU A 459 REMARK 465 ALA A 460 REMARK 465 LYS A 461 REMARK 465 THR A 764 REMARK 465 ALA A 765 REMARK 465 PRO A 766 REMARK 465 THR A 767 REMARK 465 GLN A 768 REMARK 465 PRO A 769 REMARK 465 MET A 770 REMARK 465 TYR A 771 REMARK 465 GLU A 772 REMARK 465 THR A 773 REMARK 465 GLU A 774 REMARK 465 LYS A 775 REMARK 465 PRO A 776 REMARK 465 LEU A 777 REMARK 465 GLU A 778 REMARK 465 PRO A 779 REMARK 465 ALA A 780 REMARK 465 PRO A 781 REMARK 465 VAL A 782 REMARK 465 ALA A 783 REMARK 465 PRO A 784 REMARK 465 SER A 785 REMARK 465 TYR A 786 REMARK 465 GLU A 787 REMARK 465 ASN A 788 REMARK 465 GLU A 789 REMARK 465 PRO A 790 REMARK 465 THR A 791 REMARK 465 PRO A 792 REMARK 465 PRO A 793 REMARK 465 VAL A 794 REMARK 465 LYS A 795 REMARK 465 THR A 796 REMARK 465 PRO A 797 REMARK 465 GLU B 449 REMARK 465 ALA B 450 REMARK 465 LYS B 451 REMARK 465 LEU B 452 REMARK 465 ALA B 453 REMARK 465 LYS B 454 REMARK 465 TYR B 455 REMARK 465 GLU B 456 REMARK 465 ALA B 457 REMARK 465 ASP B 458 REMARK 465 LEU B 459 REMARK 465 ALA B 460 REMARK 465 LYS B 461 REMARK 465 TYR B 462 REMARK 465 LYS B 463 REMARK 465 LYS B 464 REMARK 465 GLU B 465 REMARK 465 PHE B 466 REMARK 465 ALA B 467 REMARK 465 VAL B 761 REMARK 465 ALA B 762 REMARK 465 PRO B 763 REMARK 465 THR B 764 REMARK 465 ALA B 765 REMARK 465 PRO B 766 REMARK 465 THR B 767 REMARK 465 GLN B 768 REMARK 465 PRO B 769 REMARK 465 MET B 770 REMARK 465 TYR B 771 REMARK 465 GLU B 772 REMARK 465 THR B 773 REMARK 465 GLU B 774 REMARK 465 LYS B 775 REMARK 465 PRO B 776 REMARK 465 LEU B 777 REMARK 465 GLU B 778 REMARK 465 PRO B 779 REMARK 465 ALA B 780 REMARK 465 PRO B 781 REMARK 465 VAL B 782 REMARK 465 ALA B 783 REMARK 465 PRO B 784 REMARK 465 SER B 785 REMARK 465 TYR B 786 REMARK 465 GLU B 787 REMARK 465 ASN B 788 REMARK 465 GLU B 789 REMARK 465 PRO B 790 REMARK 465 THR B 791 REMARK 465 PRO B 792 REMARK 465 PRO B 793 REMARK 465 VAL B 794 REMARK 465 LYS B 795 REMARK 465 THR B 796 REMARK 465 PRO B 797 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 595 -129.33 49.04 REMARK 500 THR A 611 -84.94 80.53 REMARK 500 THR A 619 -106.47 -106.70 REMARK 500 ASP A 659 125.58 170.83 REMARK 500 ASP B 483 133.53 -21.91 REMARK 500 ASP B 507 135.55 -37.79 REMARK 500 TYR B 513 -177.44 -56.85 REMARK 500 ASN B 595 -133.56 57.24 REMARK 500 THR B 611 -85.55 84.44 REMARK 500 THR B 619 -98.22 -112.87 REMARK 500 LEU B 639 33.54 -90.22 REMARK 500 ASP B 659 118.89 -177.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 POTASSIUM ION (K): POSITIONED BETWEEN CHAIN A AND CHAIN B REMARK 600 GLYCEROL (GOL): TWO GLYCEROL MOLECULES ARE MODELLED IN THE REMARK 600 CAVITY CLOSE TO THE CALCIUM ION REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1765 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 648 O REMARK 620 2 SER A 648 OG 71.7 REMARK 620 3 ASN A 650 OD1 79.2 91.2 REMARK 620 4 GLU A 664 OE1 75.9 147.5 84.8 REMARK 620 5 HOH A2088 O 147.5 84.4 79.5 126.1 REMARK 620 6 HOH A2100 O 156.2 131.0 104.3 81.0 54.4 REMARK 620 7 HOH A2159 O 92.1 81.1 169.9 98.1 106.0 85.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1762 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 712 OG1 REMARK 620 2 THR A 712 N 51.9 REMARK 620 3 HOH A2139 O 123.1 83.5 REMARK 620 4 THR B 712 N 112.7 164.2 110.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1763 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 648 O REMARK 620 2 SER B 648 OG 71.4 REMARK 620 3 ASN B 650 OD1 78.5 90.4 REMARK 620 4 GLU B 664 OE1 78.1 148.6 90.9 REMARK 620 5 HOH B2054 O 142.3 81.4 76.0 129.2 REMARK 620 6 HOH B2057 O 150.8 137.0 103.6 72.8 63.6 REMARK 620 7 HOH B2098 O 100.1 81.4 171.6 96.9 101.2 81.8 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1766 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1767 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS THE SEQUENCE FOR THE WHOLE SSPB PROTEIN SINCE REMARK 999 THERE IS NO SPECIFIC ENTRY FOR ONLY THE V-DOMAIN ITSELF DBREF 2WD6 A 449 797 UNP P16952 SSP5_STRGN 449 797 DBREF 2WD6 B 449 797 UNP P16952 SSP5_STRGN 449 797 SEQRES 1 A 349 GLU ALA LYS LEU ALA LYS TYR GLU ALA ASP LEU ALA LYS SEQRES 2 A 349 TYR LYS LYS GLU PHE ALA ALA TYR THR ALA ALA LEU ALA SEQRES 3 A 349 GLU ALA GLU SER LYS LYS LYS GLN ASP GLY TYR LEU SER SEQRES 4 A 349 GLU PRO ARG SER GLN SER LEU ASN PHE LYS SER GLU PRO SEQRES 5 A 349 ASN ALA ILE ARG THR ILE ASP SER SER VAL HIS GLN TYR SEQRES 6 A 349 GLY GLN GLN GLU LEU ASP ALA LEU VAL LYS SER TRP GLY SEQRES 7 A 349 ILE SER PRO THR ASN PRO ASP ARG LYS LYS SER ARG ALA SEQRES 8 A 349 TYR SER TYR PHE ASN ALA ILE ASN SER ASN ASN THR TYR SEQRES 9 A 349 ALA LYS LEU VAL LEU GLU LYS ASP LYS PRO VAL ASP VAL SEQRES 10 A 349 THR TYR THR GLY LEU LYS ASN SER SER PHE ASN GLY LYS SEQRES 11 A 349 LYS ILE SER LYS VAL VAL TYR THR TYR THR LEU LYS GLU SEQRES 12 A 349 THR GLY PHE ASN ASP GLY THR LYS MET THR MET PHE ALA SEQRES 13 A 349 SER SER ASP PRO THR VAL THR ALA TRP TYR ASN ASP TYR SEQRES 14 A 349 PHE THR SER THR ASN ILE ASN VAL LYS VAL LYS PHE TYR SEQRES 15 A 349 ASP GLU GLU GLY GLN LEU MET ASN LEU THR GLY GLY LEU SEQRES 16 A 349 VAL ASN PHE SER SER LEU ASN ARG GLY ASN GLY SER GLY SEQRES 17 A 349 ALA ILE ASP LYS ASP ALA ILE GLU SER VAL ARG ASN PHE SEQRES 18 A 349 ASN GLY ARG TYR ILE PRO ILE SER GLY SER SER ILE LYS SEQRES 19 A 349 ILE HIS GLU ASN ASN SER ALA TYR ALA ASP SER SER ASN SEQRES 20 A 349 ALA GLU LYS SER LEU GLY ALA ARG TRP ASN THR SER GLU SEQRES 21 A 349 TRP ASP THR THR SER SER PRO ASN ASN TRP TYR GLY ALA SEQRES 22 A 349 ILE VAL GLY GLU ILE THR GLN SER GLU ILE SER PHE ASN SEQRES 23 A 349 MET ALA SER SER LYS SER GLY ASN ILE TRP PHE ALA PHE SEQRES 24 A 349 ASN SER ASN ILE ASN ALA ILE GLY VAL PRO THR LYS PRO SEQRES 25 A 349 VAL ALA PRO THR ALA PRO THR GLN PRO MET TYR GLU THR SEQRES 26 A 349 GLU LYS PRO LEU GLU PRO ALA PRO VAL ALA PRO SER TYR SEQRES 27 A 349 GLU ASN GLU PRO THR PRO PRO VAL LYS THR PRO SEQRES 1 B 349 GLU ALA LYS LEU ALA LYS TYR GLU ALA ASP LEU ALA LYS SEQRES 2 B 349 TYR LYS LYS GLU PHE ALA ALA TYR THR ALA ALA LEU ALA SEQRES 3 B 349 GLU ALA GLU SER LYS LYS LYS GLN ASP GLY TYR LEU SER SEQRES 4 B 349 GLU PRO ARG SER GLN SER LEU ASN PHE LYS SER GLU PRO SEQRES 5 B 349 ASN ALA ILE ARG THR ILE ASP SER SER VAL HIS GLN TYR SEQRES 6 B 349 GLY GLN GLN GLU LEU ASP ALA LEU VAL LYS SER TRP GLY SEQRES 7 B 349 ILE SER PRO THR ASN PRO ASP ARG LYS LYS SER ARG ALA SEQRES 8 B 349 TYR SER TYR PHE ASN ALA ILE ASN SER ASN ASN THR TYR SEQRES 9 B 349 ALA LYS LEU VAL LEU GLU LYS ASP LYS PRO VAL ASP VAL SEQRES 10 B 349 THR TYR THR GLY LEU LYS ASN SER SER PHE ASN GLY LYS SEQRES 11 B 349 LYS ILE SER LYS VAL VAL TYR THR TYR THR LEU LYS GLU SEQRES 12 B 349 THR GLY PHE ASN ASP GLY THR LYS MET THR MET PHE ALA SEQRES 13 B 349 SER SER ASP PRO THR VAL THR ALA TRP TYR ASN ASP TYR SEQRES 14 B 349 PHE THR SER THR ASN ILE ASN VAL LYS VAL LYS PHE TYR SEQRES 15 B 349 ASP GLU GLU GLY GLN LEU MET ASN LEU THR GLY GLY LEU SEQRES 16 B 349 VAL ASN PHE SER SER LEU ASN ARG GLY ASN GLY SER GLY SEQRES 17 B 349 ALA ILE ASP LYS ASP ALA ILE GLU SER VAL ARG ASN PHE SEQRES 18 B 349 ASN GLY ARG TYR ILE PRO ILE SER GLY SER SER ILE LYS SEQRES 19 B 349 ILE HIS GLU ASN ASN SER ALA TYR ALA ASP SER SER ASN SEQRES 20 B 349 ALA GLU LYS SER LEU GLY ALA ARG TRP ASN THR SER GLU SEQRES 21 B 349 TRP ASP THR THR SER SER PRO ASN ASN TRP TYR GLY ALA SEQRES 22 B 349 ILE VAL GLY GLU ILE THR GLN SER GLU ILE SER PHE ASN SEQRES 23 B 349 MET ALA SER SER LYS SER GLY ASN ILE TRP PHE ALA PHE SEQRES 24 B 349 ASN SER ASN ILE ASN ALA ILE GLY VAL PRO THR LYS PRO SEQRES 25 B 349 VAL ALA PRO THR ALA PRO THR GLN PRO MET TYR GLU THR SEQRES 26 B 349 GLU LYS PRO LEU GLU PRO ALA PRO VAL ALA PRO SER TYR SEQRES 27 B 349 GLU ASN GLU PRO THR PRO PRO VAL LYS THR PRO HET CA A1765 1 HET GOL A1766 6 HET GOL A1767 6 HET K B1762 1 HET CA B1763 1 HET GOL B1764 6 HET GOL B1765 6 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 2(CA 2+) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 K K 1+ FORMUL 10 HOH *281(H2 O) HELIX 1 1 TYR A 462 LYS A 479 1 18 HELIX 2 2 GLY A 514 TRP A 525 1 12 HELIX 3 3 ASP A 533 ASN A 547 1 15 HELIX 4 4 GLU A 697 GLY A 701 5 5 HELIX 5 5 ASN A 705 TRP A 709 5 5 HELIX 6 6 ASN A 716 ALA A 721 5 6 HELIX 7 7 ALA B 468 LYS B 479 1 12 HELIX 8 8 GLY B 514 SER B 524 1 11 HELIX 9 9 ASP B 533 ASN B 547 1 15 HELIX 10 10 GLU B 697 GLY B 701 5 5 HELIX 11 11 ASN B 705 TRP B 709 5 5 HELIX 12 12 ASN B 716 ALA B 721 5 6 SHEET 1 AA 3 LEU A 494 ASN A 495 0 SHEET 2 AA 3 SER A 574 PHE A 575 -1 O SER A 574 N ASN A 495 SHEET 3 AA 3 LYS A 578 LYS A 579 -1 O LYS A 578 N PHE A 575 SHEET 1 AB 6 ILE A 503 THR A 505 0 SHEET 2 AB 6 VAL A 563 THR A 568 -1 O THR A 566 N THR A 505 SHEET 3 AB 6 LYS A 582 THR A 592 -1 O VAL A 583 N TYR A 567 SHEET 4 AB 6 SER A 620 TYR A 630 -1 O ASN A 622 N LYS A 590 SHEET 5 AB 6 GLU A 730 SER A 738 -1 O ILE A 731 N VAL A 627 SHEET 6 AB 6 ILE A 663 ARG A 667 -1 O ILE A 663 N SER A 738 SHEET 1 AC 5 ILE A 503 THR A 505 0 SHEET 2 AC 5 VAL A 563 THR A 568 -1 O THR A 566 N THR A 505 SHEET 3 AC 5 LYS A 582 THR A 592 -1 O VAL A 583 N TYR A 567 SHEET 4 AC 5 SER A 620 TYR A 630 -1 O ASN A 622 N LYS A 590 SHEET 5 AC 5 LEU A 636 MET A 637 -1 N MET A 637 O PHE A 629 SHEET 1 AD 4 ALA A 553 GLU A 558 0 SHEET 2 AD 4 LYS A 599 ALA A 604 -1 O MET A 600 N LEU A 557 SHEET 3 AD 4 ALA A 612 ASN A 615 -1 O TRP A 613 N PHE A 603 SHEET 4 AD 4 ASN A 742 PHE A 745 -1 O ILE A 743 N TYR A 614 SHEET 1 AE 3 LEU A 643 PHE A 646 0 SHEET 2 AE 3 ILE A 722 GLU A 725 -1 O ILE A 722 N PHE A 646 SHEET 3 AE 3 ARG A 672 ILE A 674 -1 O ARG A 672 N GLU A 725 SHEET 1 AF 2 ILE A 681 HIS A 684 0 SHEET 2 AF 2 SER A 688 ALA A 691 -1 O SER A 688 N HIS A 684 SHEET 1 BA 3 LEU B 494 ASN B 495 0 SHEET 2 BA 3 SER B 574 PHE B 575 -1 O SER B 574 N ASN B 495 SHEET 3 BA 3 LYS B 578 LYS B 579 -1 O LYS B 578 N PHE B 575 SHEET 1 BB 6 ILE B 503 THR B 505 0 SHEET 2 BB 6 VAL B 563 THR B 568 -1 O THR B 566 N THR B 505 SHEET 3 BB 6 LYS B 582 THR B 592 -1 O VAL B 583 N TYR B 567 SHEET 4 BB 6 SER B 620 TYR B 630 -1 O ASN B 622 N LYS B 590 SHEET 5 BB 6 ILE B 731 SER B 738 -1 O ILE B 731 N VAL B 627 SHEET 6 BB 6 ILE B 663 ARG B 667 -1 O ILE B 663 N SER B 738 SHEET 1 BC 4 ALA B 553 GLU B 558 0 SHEET 2 BC 4 LYS B 599 ALA B 604 -1 O MET B 600 N LEU B 557 SHEET 3 BC 4 ALA B 612 ASN B 615 -1 O TRP B 613 N PHE B 603 SHEET 4 BC 4 ASN B 742 PHE B 745 -1 O ILE B 743 N TYR B 614 SHEET 1 BD 3 LEU B 643 PHE B 646 0 SHEET 2 BD 3 ILE B 722 GLU B 725 -1 O ILE B 722 N PHE B 646 SHEET 3 BD 3 ARG B 672 ILE B 674 -1 O ARG B 672 N GLU B 725 SHEET 1 BE 2 ILE B 681 HIS B 684 0 SHEET 2 BE 2 SER B 688 ALA B 691 -1 O SER B 688 N HIS B 684 LINK O SER A 648 CA CA A1765 1555 1555 2.27 LINK OG SER A 648 CA CA A1765 1555 1555 2.34 LINK OD1 ASN A 650 CA CA A1765 1555 1555 2.35 LINK OE1 GLU A 664 CA CA A1765 1555 1555 2.44 LINK OG1 THR A 712 K K B1762 1555 1555 3.42 LINK N THR A 712 K K B1762 1555 1555 3.11 LINK CA CA A1765 O HOH A2088 1555 1555 2.73 LINK CA CA A1765 O HOH A2100 1555 1555 2.62 LINK CA CA A1765 O HOH A2159 1555 1555 2.40 LINK O HOH A2139 K K B1762 1555 1555 3.44 LINK O SER B 648 CA CA B1763 1555 1555 2.35 LINK OG SER B 648 CA CA B1763 1555 1555 2.29 LINK OD1 ASN B 650 CA CA B1763 1555 1555 2.33 LINK OE1 GLU B 664 CA CA B1763 1555 1555 2.48 LINK N THR B 712 K K B1762 1555 1555 3.16 LINK CA CA B1763 O HOH B2054 1555 1555 2.77 LINK CA CA B1763 O HOH B2057 1555 1555 2.60 LINK CA CA B1763 O HOH B2098 1555 1555 2.15 SITE 1 AC1 4 THR A 711 THR A 712 THR B 711 THR B 712 SITE 1 AC2 6 SER A 648 ASN A 650 GLU A 664 HOH A2088 SITE 2 AC2 6 HOH A2100 HOH A2159 SITE 1 AC3 6 SER B 648 ASN B 650 GLU B 664 HOH B2054 SITE 2 AC3 6 HOH B2057 HOH B2098 SITE 1 AC4 6 SER A 541 TYR A 542 ALA A 545 TRP B 704 SITE 2 AC4 6 ASN B 716 GOL B1765 SITE 1 AC5 4 TRP A 704 ASN A 716 GOL A1767 ALA B 545 SITE 1 AC6 8 TYR A 542 TRP A 613 ASN A 742 GLU B 708 SITE 2 AC6 8 SER B 714 PRO B 715 GOL B1764 HOH B2085 SITE 1 AC7 6 GLU A 708 SER A 714 GOL A1766 TYR B 542 SITE 2 AC7 6 TRP B 613 ASN B 742 CRYST1 110.170 110.170 121.490 90.00 90.00 120.00 P 65 12 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 0.009077 0.005241 0.000000 0.00000 SCALE2 0.000000 0.010481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008231 0.00000