HEADER CALCIUM BINDING PROTEIN 01-FEB-99 1B8L TITLE CALCIUM-BOUND D51A/E101D/F102W TRIPLE MUTANT OF BETA CARP 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.HO,Q.LI,J.D.POTTER,G.N.PHILLIPS JR. REVDAT 6 09-AUG-23 1B8L 1 REMARK LINK REVDAT 5 24-JUL-19 1B8L 1 REMARK REVDAT 4 07-MAR-18 1B8L 1 REMARK REVDAT 3 24-FEB-09 1B8L 1 VERSN REVDAT 2 03-MAY-05 1B8L 1 COMPND AUTHOR JRNL REMARK REVDAT 2 2 1 LINK REVDAT 1 05-OCT-99 1B8L 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 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) : 0.167 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.700 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 950 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8141 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.164 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.165 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.600 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 892 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 7671 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 970.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 794.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3903 REMARK 3 NUMBER OF RESTRAINTS : 3327 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 0.015 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.001 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.043 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.043 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.024 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.052 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 1B8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.9 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 : 9239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.03800 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: CNS, SHELX REMARK 200 STARTING MODEL: 5CPV, AUTH A.L.SWAIN,R.H.KRETSINGER, E.L.AMMA REMARK 200 REMARK 200 REMARK: ALTERNATE CONFORMATION MODELED FOR SIDE CHAIN LYS 3 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS 40% PEG REMARK 280 4000, 50 MM CACL2, 50 M PH 7.0, 4 DEGREES C, PH 6.9 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 18.64900 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: 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 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 90 OD1 REMARK 620 2 ASP A 92 OD1 80.2 REMARK 620 3 ASP A 94 OD1 89.4 96.6 REMARK 620 4 LYS A 96 O 84.9 164.7 86.7 REMARK 620 5 ASP A 101 OD2 104.0 94.7 163.8 85.5 REMARK 620 6 HOH A 118 O 170.7 97.7 81.8 97.5 85.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 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 1B8L 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 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 HET CO3 A 109 4 HET CA A 110 1 HETNAM CO3 CARBONATE ION HETNAM CA CALCIUM ION FORMUL 2 CO3 C O3 2- FORMUL 3 CA CA 2+ FORMUL 4 HOH *159(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 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 LINK OD1 ASP A 90 CA CA A 110 1555 1555 2.30 LINK OD1 ASP A 92 CA CA A 110 1555 1555 2.23 LINK OD1 ASP A 94 CA CA A 110 1555 1555 2.18 LINK O LYS A 96 CA CA A 110 1555 1555 2.30 LINK OD2 ASP A 101 CA CA A 110 1555 1555 2.26 LINK CA CA A 110 O HOH A 118 1555 1555 2.38 SITE 1 AC1 7 ALA A 13 VAL A 99 ASP A 100 HOH A 111 SITE 2 AC1 7 HOH A 127 HOH A 130 HOH A 243 SITE 1 AC2 6 ASP A 90 ASP A 92 ASP A 94 LYS A 96 SITE 2 AC2 6 ASP A 101 HOH A 118 CRYST1 34.511 37.298 37.067 90.00 113.12 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 0.028976 0.000000 0.012371 0.00000 SCALE2 0.000000 0.026811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029334 0.00000