HEADER CALCIUM BINDING PROTEIN 29-JAN-99 1B8C TITLE PARVALBUMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PARVALBUMIN); COMPND 3 CHAIN: A, B; 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 6 09-AUG-23 1B8C 1 REMARK LINK REVDAT 5 07-MAR-18 1B8C 1 REMARK REVDAT 4 24-FEB-09 1B8C 1 VERSN REVDAT 3 01-APR-03 1B8C 1 JRNL REVDAT 2 05-OCT-99 1B8C 1 JRNL REVDAT 1 02-FEB-99 1B8C 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.196 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.197 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1266 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10920 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.192 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.192 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.600 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1220 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1612 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1830.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1588.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7479 REMARK 3 NUMBER OF RESTRAINTS : 6631 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.014 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.034 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.042 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.075 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 13158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08500 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, SHELX 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 (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: 40% PEG REMARK 280 4000, 200 MM MGCL2, 50 M PH 7. THE CRYSTALS WERE GROWN AT 4 REMARK 280 DEGREES C., PH 7.0 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 25.10550 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 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 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 ALA A 3 107.72 -52.53 REMARK 500 GLN A 52 -3.62 72.08 REMARK 500 ASP A 53 139.16 176.42 REMARK 500 ASP B 252 116.50 179.52 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 MG A 308 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD2 REMARK 620 2 ASP A 90 OD1 9.1 REMARK 620 3 ASP A 92 OD1 95.7 94.5 REMARK 620 4 ASP A 94 OD1 72.9 81.8 86.8 REMARK 620 5 LYS A 96 O 82.0 84.7 170.0 83.2 REMARK 620 6 ASP A 101 OD2 117.5 108.7 95.5 168.9 94.2 REMARK 620 7 HOH A 580 O 152.1 161.1 91.0 80.5 86.7 88.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 309 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 289 OD2 REMARK 620 2 ASP B 289 OD1 12.8 REMARK 620 3 ASP B 291 OD1 94.1 91.3 REMARK 620 4 ASP B 293 OD1 78.7 91.2 89.6 REMARK 620 5 LYS B 295 O 80.8 84.6 173.3 85.2 REMARK 620 6 ASP B 300 OD2 122.0 109.8 93.5 158.6 92.9 REMARK 620 7 HOH B 664 O 157.1 167.9 82.0 78.7 101.0 80.8 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 MG A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 309 DBREF 1B8C A 1 108 UNP P02618 PRVB_CYPCA 1 108 DBREF 1B8C B 200 307 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 ALA 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 ASP TRP THR ALA SEQRES 9 A 108 LEU VAL LYS ALA SEQRES 1 B 108 ALA PHE ALA GLY VAL LEU ASN ASP ALA ASP ILE ALA ALA SEQRES 2 B 108 ALA LEU GLU ALA CYS LYS ALA ALA ASP SER PHE ASN HIS SEQRES 3 B 108 LYS ALA PHE PHE ALA LYS VAL GLY LEU THR SER LYS SER SEQRES 4 B 108 ALA ASP ASP VAL LYS LYS ALA PHE ALA ILE ILE ALA GLN SEQRES 5 B 108 ASP LYS SER GLY PHE ILE GLU GLU ASP GLU LEU LYS LEU SEQRES 6 B 108 PHE LEU GLN ASN PHE LYS ALA ASP ALA ARG ALA LEU THR SEQRES 7 B 108 ASP GLY GLU THR LYS THR PHE LEU LYS ALA GLY ASP SER SEQRES 8 B 108 ASP GLY ASP GLY LYS ILE GLY VAL ASP ASP TRP THR ALA SEQRES 9 B 108 LEU VAL LYS ALA HET MG A 308 1 HET MG B 309 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *255(H2 O) HELIX 1 1 ASP A 8 CYS A 18 1 11 HELIX 2 2 HIS A 26 LYS A 32 1 7 HELIX 3 3 ALA A 40 ALA A 51 1 12 HELIX 4 4 GLU A 60 ASN A 69 1 10 HELIX 5 5 ASP A 79 GLY A 89 1 11 HELIX 6 6 VAL A 99 VAL A 106 1 8 HELIX 7 7 ASP B 207 CYS B 217 1 11 HELIX 8 8 HIS B 225 VAL B 232 1 8 HELIX 9 9 ALA B 239 ALA B 250 1 12 HELIX 10 10 GLU B 259 ASN B 268 1 10 HELIX 11 11 ASP B 278 GLY B 288 1 11 HELIX 12 12 VAL B 298 VAL B 305 1 8 SHEET 1 A 2 PHE B 256 ILE B 257 0 SHEET 2 A 2 ILE B 296 GLY B 297 -1 N ILE B 296 O ILE B 257 LINK OD2 ASP A 90 MG MG A 308 1555 1555 4.03 LINK OD1 ASP A 90 MG MG A 308 1555 1555 1.88 LINK OD1 ASP A 92 MG MG A 308 1555 1555 2.06 LINK OD1 ASP A 94 MG MG A 308 1555 1555 2.11 LINK O LYS A 96 MG MG A 308 1555 1555 1.99 LINK OD2 ASP A 101 MG MG A 308 1555 1555 1.98 LINK MG MG A 308 O HOH A 580 1555 1555 2.32 LINK OD2 ASP B 289 MG MG B 309 1555 1555 3.99 LINK OD1 ASP B 289 MG MG B 309 1555 1555 1.88 LINK OD1 ASP B 291 MG MG B 309 1555 1555 2.16 LINK OD1 ASP B 293 MG MG B 309 1555 1555 2.22 LINK O LYS B 295 MG MG B 309 1555 1555 1.91 LINK OD2 ASP B 300 MG MG B 309 1555 1555 2.00 LINK MG MG B 309 O HOH B 664 1555 1555 1.99 SITE 1 AC1 6 ASP A 90 ASP A 92 ASP A 94 LYS A 96 SITE 2 AC1 6 ASP A 101 HOH A 580 SITE 1 AC2 6 ASP B 289 ASP B 291 ASP B 293 LYS B 295 SITE 2 AC2 6 ASP B 300 HOH B 664 CRYST1 35.231 50.211 55.374 90.00 99.22 90.00 P 1 21 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 0.028384 0.000000 0.004607 0.00000 SCALE2 0.000000 0.019916 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018295 0.00000