HEADER SUGAR BINDING PROTEIN 09-APR-08 2VRP TITLE STRUCTURE OF RHODOCYTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGRETIN ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHODOCYTIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AGGRETIN BETA CHAIN; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: RESIDUES 24-146; COMPND 9 SYNONYM: RHODOCYTIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CALLOSELASMA RHODOSTOMA; SOURCE 3 ORGANISM_COMMON: MALAYAN PIT VIPER; SOURCE 4 ORGANISM_TAXID: 8717; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CALLOSELASMA RHODOSTOMA; SOURCE 7 ORGANISM_COMMON: MALAYAN PIT VIPER; SOURCE 8 ORGANISM_TAXID: 8717 KEYWDS C-TYPE LECTIN-LIKE, SUGAR-BINDING PROTEIN, LECTIN, CLEC-2, VENOM, KEYWDS 2 AGGRETIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.A.WATSON,C.A.O'CALLAGHAN REVDAT 5 13-DEC-23 2VRP 1 LINK REVDAT 4 13-JUL-11 2VRP 1 VERSN REVDAT 3 24-FEB-09 2VRP 1 VERSN REVDAT 2 15-JUL-08 2VRP 1 KEYWDS REVDAT 1 08-JUL-08 2VRP 0 JRNL AUTH A.A.WATSON,J.A.EBLE,C.A.O'CALLAGHAN JRNL TITL CRYSTAL STRUCTURE OF RHODOCYTIN, A LIGAND FOR THE JRNL TITL 2 PLATELET-ACTIVATING RECEPTOR CLEC-2. JRNL REF PROTEIN SCI. V. 17 1611 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18583525 JRNL DOI 10.1110/PS.035568.108 REMARK 2 REMARK 2 RESOLUTION. 2.41 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 12040 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 618 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) : 2.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 698 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 44 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) : 38.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.56000 REMARK 3 B33 (A**2) : -0.67000 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): 0.396 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.287 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.272 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.314 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2173 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2947 ; 1.916 ; 1.900 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 8.822 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;38.547 ;24.746 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 353 ;22.436 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;20.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 284 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1709 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 987 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1405 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 89 ; 0.178 ; 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): 52 ; 0.294 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.273 ; 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): 1273 ; 0.872 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2030 ; 1.704 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 2.161 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 917 ; 3.438 ; 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 1 A 132 5 REMARK 3 1 B 1 B 132 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 120 ; 1.15 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 136 ; 1.86 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 120 ; 1.46 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 136 ; 2.23 ; 10.00 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 1 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0350 -13.2730 -6.2032 REMARK 3 T TENSOR REMARK 3 T11: -0.0530 T22: 0.0210 REMARK 3 T33: 0.0897 T12: -0.0226 REMARK 3 T13: -0.0328 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.9940 L22: 1.8865 REMARK 3 L33: 6.8846 L12: 0.1600 REMARK 3 L13: 0.5947 L23: 0.5894 REMARK 3 S TENSOR REMARK 3 S11: -0.0636 S12: 0.0693 S13: -0.0516 REMARK 3 S21: 0.0313 S22: 0.1229 S23: 0.1185 REMARK 3 S31: 0.0842 S32: 0.0554 S33: -0.0593 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 1 B 123 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1874 -12.4639 22.6175 REMARK 3 T TENSOR REMARK 3 T11: -0.0055 T22: -0.0021 REMARK 3 T33: 0.1026 T12: -0.0207 REMARK 3 T13: 0.0612 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.3716 L22: 1.6940 REMARK 3 L33: 8.2292 L12: 0.1333 REMARK 3 L13: -0.2566 L23: -1.2028 REMARK 3 S TENSOR REMARK 3 S11: 0.0773 S12: -0.0501 S13: -0.1121 REMARK 3 S21: 0.3717 S22: -0.0515 S23: -0.1382 REMARK 3 S31: -0.0406 S32: -0.2186 S33: -0.0258 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 2VRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290035882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13367 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 94.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB REMARK 200 ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, 5% 2-PROPANOL, REMARK 280 PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.96650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.68400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.49800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.96650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.68400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.49800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.96650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.68400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.49800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.96650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.68400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.49800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.9 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 61.93300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 1 REMARK 465 LEU A 2 REMARK 465 GLU A 3 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 ALA A 65 N - CA - C ANGL. DEV. = -18.0 DEGREES REMARK 500 ASP A 66 N - CA - C ANGL. DEV. = 18.5 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 GLN A 14 -13.01 71.94 REMARK 500 GLU A 37 -128.89 43.95 REMARK 500 GLU A 63 6.29 -66.33 REMARK 500 ASP A 66 41.99 37.91 REMARK 500 ASN A 78 -41.52 -135.62 REMARK 500 GLU A 80 170.21 -54.20 REMARK 500 ASN A 97 75.67 -119.90 REMARK 500 LYS A 104 62.59 -103.25 REMARK 500 ARG A 116 -64.94 -129.96 REMARK 500 SER B 4 141.49 -38.39 REMARK 500 GLU B 19 97.70 -161.17 REMARK 500 ALA B 61 74.42 -116.34 REMARK 500 ASN B 86 -69.00 -98.53 REMARK 500 ASP B 89 65.03 -157.53 REMARK 500 GLU B 92 34.50 70.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN B 91 GLU B 92 40.41 REMARK 500 REMARK 500 REMARK: NULL 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 NA B1124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B1127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1126 REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST THREE RESIDUES OF THE Q9I840 SEQUENCE OF CHAIN A ARE REMARK 999 ABSENT FROM THE STRUCTURE. REMARK 999 FIRST TWENTY-THREE RESIDUES OF THE Q9I841 SEQUENCE OF REMARK 999 CHAIN B ARE ABSENT FROM THE STRUCTURE, BECAUSE THESE REMARK 999 RESIDUES ARE ABSENT FROM THE NATIVE PROTEIN (AS DETERMINED REMARK 999 BY N-TERMINAL SEQUENCING, PMID 11728470) DBREF 2VRP A 1 136 UNP Q9I841 Q9I841_AGKRH 1 136 DBREF 2VRP B 1 123 UNP Q9I840 Q9I840_AGKRH 24 146 SEQRES 1 A 136 GLY LEU GLU ASP CYS ASP PHE GLY TRP SER PRO TYR ASP SEQRES 2 A 136 GLN HIS CYS TYR GLN ALA PHE ASN GLU GLN LYS THR TRP SEQRES 3 A 136 ASP GLU ALA GLU LYS PHE CYS ARG ALA GLN GLU ASN GLY SEQRES 4 A 136 ALA HIS LEU ALA SER ILE GLU SER ASN GLY GLU ALA ASP SEQRES 5 A 136 PHE VAL SER TRP LEU ILE SER GLN LYS ASP GLU LEU ALA SEQRES 6 A 136 ASP GLU ASP TYR VAL TRP ILE GLY LEU ARG ALA GLN ASN SEQRES 7 A 136 LYS GLU GLN GLN CYS SER SER GLU TRP SER ASP GLY SER SEQRES 8 A 136 SER VAL SER TYR GLU ASN LEU ILE ASP LEU HIS THR LYS SEQRES 9 A 136 LYS CYS GLY ALA LEU GLU LYS LEU THR GLY PHE ARG LYS SEQRES 10 A 136 TRP VAL ASN TYR TYR CYS GLU GLN MET HIS ALA PHE VAL SEQRES 11 A 136 CYS LYS LEU LEU PRO TYR SEQRES 1 B 123 ASP CYS PRO SER GLY TRP SER SER TYR GLU GLY HIS CYS SEQRES 2 B 123 TYR LYS PRO PHE ASN GLU PRO LYS ASN TRP ALA ASP ALA SEQRES 3 B 123 GLU ARG PHE CYS LYS LEU GLN PRO LYS HIS SER HIS LEU SEQRES 4 B 123 VAL SER PHE GLN SER ALA GLU GLU ALA ASP PHE VAL VAL SEQRES 5 B 123 LYS LEU THR ARG PRO ARG LEU LYS ALA ASN LEU VAL TRP SEQRES 6 B 123 MET GLY LEU SER ASN ILE TRP HIS GLY CYS ASN TRP GLN SEQRES 7 B 123 TRP SER ASP GLY ALA ARG LEU ASN TYR LYS ASP TRP GLN SEQRES 8 B 123 GLU GLN SER GLU CYS LEU ALA PHE ARG GLY VAL HIS THR SEQRES 9 B 123 GLU TRP LEU ASN MET ASP CYS SER SER THR CYS SER PHE SEQRES 10 B 123 VAL CYS LYS PHE LYS ALA HET NA A1137 1 HET NA A1138 1 HET NA B1124 1 HET CL B1125 1 HET CL B1126 1 HET NA B1127 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 3 NA 4(NA 1+) FORMUL 6 CL 2(CL 1-) FORMUL 9 HOH *44(H2 O) HELIX 1 1 THR A 25 ALA A 35 1 11 HELIX 2 2 SER A 47 LYS A 61 1 15 HELIX 3 3 LEU A 112 GLY A 114 5 3 HELIX 4 4 ASN B 22 LEU B 32 1 11 HELIX 5 5 SER B 44 LYS B 60 1 17 SHEET 1 AA 4 SER A 10 TYR A 12 0 SHEET 2 AA 4 HIS A 15 LYS A 24 -1 O HIS A 15 N TYR A 12 SHEET 3 AA 4 HIS A 127 LEU A 133 -1 O HIS A 127 N LYS A 24 SHEET 4 AA 4 HIS A 41 LEU A 42 -1 O HIS A 41 N LYS A 132 SHEET 1 AB 4 SER A 10 TYR A 12 0 SHEET 2 AB 4 HIS A 15 LYS A 24 -1 O HIS A 15 N TYR A 12 SHEET 3 AB 4 HIS A 127 LEU A 133 -1 O HIS A 127 N LYS A 24 SHEET 4 AB 4 TYR A 69 ALA A 76 1 O TYR A 69 N ALA A 128 SHEET 1 BA 4 SER B 7 TYR B 9 0 SHEET 2 BA 4 HIS B 12 LYS B 21 -1 O HIS B 12 N TYR B 9 SHEET 3 BA 4 CYS B 115 LYS B 122 -1 O CYS B 115 N LYS B 21 SHEET 4 BA 4 HIS B 38 LEU B 39 -1 O HIS B 38 N LYS B 120 SHEET 1 BB 6 SER B 7 TYR B 9 0 SHEET 2 BB 6 HIS B 12 LYS B 21 -1 O HIS B 12 N TYR B 9 SHEET 3 BB 6 CYS B 115 LYS B 122 -1 O CYS B 115 N LYS B 21 SHEET 4 BB 6 LEU B 63 SER B 69 1 O LEU B 63 N SER B 116 SHEET 5 BB 6 GLU B 95 ARG B 100 -1 O LEU B 97 N MET B 66 SHEET 6 BB 6 TRP B 106 ASP B 110 -1 O LEU B 107 N ALA B 98 SSBOND 1 CYS A 5 CYS A 16 1555 1555 2.10 SSBOND 2 CYS A 33 CYS A 131 1555 1555 2.14 SSBOND 3 CYS A 83 CYS B 75 1555 1555 2.04 SSBOND 4 CYS A 106 CYS A 123 1555 1555 2.06 SSBOND 5 CYS B 2 CYS B 13 1555 1555 2.06 SSBOND 6 CYS B 30 CYS B 119 1555 1555 2.10 SSBOND 7 CYS B 96 CYS B 111 1555 1555 2.05 LINK OD2 ASP B 1 NA NA B1124 1555 1555 2.20 CISPEP 1 LEU A 64 ALA A 65 0 -27.28 CISPEP 2 ALA A 65 ASP A 66 0 -16.03 CISPEP 3 GLN A 77 ASN A 78 0 -1.18 CISPEP 4 ASN A 78 LYS A 79 0 -19.66 CISPEP 5 LYS B 60 ALA B 61 0 -1.03 SITE 1 AC1 2 ASP B 1 SER B 8 SITE 1 AC2 1 GLY B 5 SITE 1 AC3 2 SER A 91 SER A 92 SITE 1 AC4 6 ASN B 70 ILE B 71 TRP B 72 HIS B 73 SITE 2 AC4 6 SER B 94 GLU B 95 SITE 1 AC5 1 ASN B 18 CRYST1 61.933 89.368 120.996 90.00 90.00 90.00 I 2 2 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 0.016146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008265 0.00000