HEADER CALCIUM BINDING PROTEIN 02-FEB-99 1B8R TITLE PARVALBUMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PARVALBUMIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYPRINUS CARPIO; SOURCE 3 ORGANISM_COMMON: COMMON CARP; SOURCE 4 ORGANISM_TAXID: 7962; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CALCIUM BINDING PROTEIN, EF-HAND PROTEINS, PARVALBUMIN, CALCIUM- KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.S.CATES,M.B.BERRY,E.L.HO,Q.LI,J.D.POTTER,G.N.PHILLIPS JR. REVDAT 7 09-AUG-23 1B8R 1 REMARK LINK REVDAT 6 07-MAR-18 1B8R 1 REMARK REVDAT 5 04-OCT-17 1B8R 1 REMARK REVDAT 4 24-FEB-09 1B8R 1 VERSN REVDAT 3 01-APR-03 1B8R 1 JRNL REVDAT 2 05-OCT-99 1B8R 1 JRNL REVDAT 1 09-FEB-99 1B8R 0 JRNL AUTH M.S.CATES,M.B.BERRY,E.L.HO,Q.LI,J.D.POTTER,G.N.PHILLIPS JR. JRNL TITL METAL-ION AFFINITY AND SPECIFICITY IN EF-HAND PROTEINS: JRNL TITL 2 COORDINATION GEOMETRY AND DOMAIN PLASTICITY IN PARVALBUMIN. JRNL REF STRUCTURE FOLD.DES. V. 7 1269 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10545326 JRNL DOI 10.1016/S0969-2126(00)80060-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.L.SWAIN,R.H.KRETSINGER,E.L.AMMA REMARK 1 TITL RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND REMARK 1 TITL 2 CADMIUM- SUBSTITUTED CARP PARVALBUMIN USING X-RAY REMARK 1 TITL 3 CRYSTALLOGRAPHIC DATA AT 1.6 ANGSTROM RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 264 16620 1989 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 6147 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 SET) : 0.177 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.578 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.66 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.362 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07000 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 5CPV, AUTH A.L.SWAIN,R.H.KRETSINGER, E.L.AMMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: PH 5.0 - REMARK 280 5.5, 3.1 - 3.2 M AMMONIUM SULFATE 0.05 - 0.10 M CACL2, ROOM REMARK 280 TEMPERATURE, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 14.42500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.42500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.29500 REMARK 290 SMTRY3 4 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: 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 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 VAL A 5 -43.17 -135.94 REMARK 500 REMARK 500 REMARK: NULL 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 A 110 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 ASP A 53 OD1 90.1 REMARK 620 3 SER A 55 OG 90.0 75.2 REMARK 620 4 PHE A 57 O 77.0 153.6 81.8 REMARK 620 5 GLU A 59 OE1 170.1 96.6 84.7 94.0 REMARK 620 6 GLU A 62 OE1 105.4 122.4 155.7 83.5 77.1 REMARK 620 7 GLU A 62 OE2 104.6 73.5 145.3 131.8 84.4 49.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 109 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD1 REMARK 620 2 ASP A 92 OD1 79.0 REMARK 620 3 ASP A 94 OD1 86.0 76.0 REMARK 620 4 LYS A 96 O 90.5 152.8 78.3 REMARK 620 5 GLU A 101 OE1 117.2 121.4 152.0 85.7 REMARK 620 6 GLU A 101 OE2 86.4 78.5 154.3 126.2 50.0 REMARK 620 7 HOH A 131 O 159.1 93.8 73.1 87.2 83.4 111.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 110 DBREF 1B8R A 1 108 UNP P02618 PRVB_CYPCA 1 108 SEQRES 1 A 108 ALA PHE ALA GLY VAL LEU ASN ASP ALA ASP ILE ALA ALA SEQRES 2 A 108 ALA LEU GLU ALA CYS LYS ALA ALA ASP SER PHE ASN HIS SEQRES 3 A 108 LYS ALA PHE PHE ALA LYS VAL GLY LEU THR SER LYS SER SEQRES 4 A 108 ALA ASP ASP VAL LYS LYS ALA PHE ALA ILE ILE ASP GLN SEQRES 5 A 108 ASP LYS SER GLY PHE ILE GLU GLU ASP GLU LEU LYS LEU SEQRES 6 A 108 PHE LEU GLN ASN PHE LYS ALA ASP ALA ARG ALA LEU THR SEQRES 7 A 108 ASP GLY GLU THR LYS THR PHE LEU LYS ALA GLY ASP SER SEQRES 8 A 108 ASP GLY ASP GLY LYS ILE GLY VAL ASP GLU TRP THR ALA SEQRES 9 A 108 LEU VAL LYS ALA HET CA A 109 1 HET CA A 110 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *89(H2 O) HELIX 1 1 ASP A 8 CYS A 18 1 11 HELIX 2 2 HIS A 26 VAL A 33 1 8 HELIX 3 3 ALA A 40 ILE A 50 1 11 HELIX 4 4 GLU A 60 LEU A 63 1 4 HELIX 5 5 PHE A 66 ASN A 69 5 4 HELIX 6 6 ASP A 79 GLY A 89 1 11 HELIX 7 7 VAL A 99 VAL A 106 1 8 SHEET 1 A 2 PHE A 57 ILE A 58 0 SHEET 2 A 2 ILE A 97 GLY A 98 -1 O ILE A 97 N ILE A 58 LINK OD1 ASP A 51 CA CA A 110 1555 1555 2.34 LINK OD1 ASP A 53 CA CA A 110 1555 1555 2.48 LINK OG SER A 55 CA CA A 110 1555 1555 2.64 LINK O PHE A 57 CA CA A 110 1555 1555 2.38 LINK OE1 GLU A 59 CA CA A 110 1555 1555 2.53 LINK OE1 GLU A 62 CA CA A 110 1555 1555 2.54 LINK OE2 GLU A 62 CA CA A 110 1555 1555 2.66 LINK OD1 ASP A 90 CA CA A 109 1555 1555 2.39 LINK OD1 ASP A 92 CA CA A 109 1555 1555 2.55 LINK OD1 ASP A 94 CA CA A 109 1555 1555 2.45 LINK O LYS A 96 CA CA A 109 1555 1555 2.38 LINK OE1 GLU A 101 CA CA A 109 1555 1555 2.50 LINK OE2 GLU A 101 CA CA A 109 1555 1555 2.62 LINK CA CA A 109 O HOH A 131 1555 1555 2.51 SITE 1 AC1 6 ASP A 90 ASP A 92 ASP A 94 LYS A 96 SITE 2 AC1 6 GLU A 101 HOH A 131 SITE 1 AC2 6 ASP A 51 ASP A 53 SER A 55 PHE A 57 SITE 2 AC2 6 GLU A 59 GLU A 62 CRYST1 28.850 60.590 54.480 90.00 94.97 90.00 C 1 2 1 4 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 0.034662 0.000000 0.003014 0.00000 SCALE2 0.000000 0.016504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018425 0.00000