HEADER CALCIUM BINDING PROTEIN 05-JAN-95 1PVB
TITLE X-RAY STRUCTURE OF A NEW CRYSTAL FORM OF PIKE 4.10
TITLE 2 PARVALBUMIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PARVALBUMIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESOX LUCIUS;
SOURCE 3 ORGANISM_COMMON: NORTHERN PIKE;
SOURCE 4 ORGANISM_TAXID: 8010
KEYWDS CALCIUM BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.P.DECLERCQ,B.TINANT,J.PARELLO
REVDAT 2 24-FEB-09 1PVB 1 VERSN
REVDAT 1 27-FEB-95 1PVB 0
JRNL AUTH J.P.DECLERCQ,B.TINANT,J.PARELLO
JRNL TITL X-RAY STRUCTURE OF A NEW CRYSTAL FORM OF PIKE 4.10
JRNL TITL 2 BETA PARVALBUMIN.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 52 165 1996
JRNL REFN ISSN 0907-4449
JRNL PMID 15299738
JRNL DOI 10.1107/S0907444995010006
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.P.DECLERCQ,B.TINANT,J.PARELLO,J.RAMBAUD
REMARK 1 TITL IONIC INTERACTIONS WITH PARVALBUMINS. CRYSTAL
REMARK 1 TITL 2 STRUCTURE DETERMINATION OF PIKE 4.10 PARVALBUMIN
REMARK 1 TITL 3 IN FOUR DIFFERENT IONIC ENVIRONMENTS
REMARK 1 REF J.MOL.BIOL. V. 220 1017 1991
REMARK 1 REFN ISSN 0022-2836
REMARK 1 REFERENCE 2
REMARK 1 AUTH J.P.DECLERCQ,B.TINANT,J.PARELLO,G.ETIENNE
REMARK 1 TITL CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT OF
REMARK 1 TITL 2 PIKE 4.10 PARVALBUMIN (MINOR COMPONENT FROM ESOX
REMARK 1 TITL 3 LUCIUS)
REMARK 1 REF J.MOL.BIOL. V. 202 349 1988
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.0
REMARK 3 NUMBER OF REFLECTIONS : 7774
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.168
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
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 : 805
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 3
REMARK 3 SOLVENT ATOMS : 72
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.70
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) : 0.15
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) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.36
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
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 1PVB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9484
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
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: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 25.92000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.48000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.97500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.48000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.92000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.97500
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 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 264 DISTANCE = 5.21 ANGSTROMS
REMARK 525 HOH A 271 DISTANCE = 5.51 ANGSTROMS
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 53 OD1
REMARK 620 2 GLU A 59 OE1 103.2
REMARK 620 3 GLU A 62 OE2 74.1 91.1
REMARK 620 4 ASP A 51 OD1 86.3 167.1 100.1
REMARK 620 5 SER A 55 OG 77.2 83.1 148.5 90.6
REMARK 620 6 PHE A 57 O 150.7 84.5 134.7 83.0 75.7
REMARK 620 7 GLU A 62 OE1 124.1 81.8 50.0 100.3 156.4 84.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 111 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 92 OD1
REMARK 620 2 ASP A 94 OD1 80.0
REMARK 620 3 GLU A 101 OE1 121.7 151.6
REMARK 620 4 GLU A 101 OE2 77.0 155.9 51.7
REMARK 620 5 HOH A 201 O 100.8 80.3 77.8 110.9
REMARK 620 6 ASP A 90 OD1 82.8 83.9 114.7 86.2 162.9
REMARK 620 7 MET A 96 O 154.5 77.6 83.5 122.8 87.4 82.8
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CD
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: CATION BINDING SITE OCCUPIED BY CA2+ (A 110)
REMARK 800 SITE_IDENTIFIER: EF
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: CATION BINDING SITE OCCUPIED BY CA2+ (A 111)
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 110
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 111
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH4 A 200
DBREF 1PVB A 1 108 UNP P02619 PRVB_ESOLU 1 107
SEQRES 1 A 108 ACE SER PHE ALA GLY LEU LYS ASP ALA ASP VAL ALA ALA
SEQRES 2 A 108 ALA LEU ALA ALA CYS SER ALA ALA ASP SER PHE LYS HIS
SEQRES 3 A 108 LYS GLU PHE PHE ALA LYS VAL GLY LEU ALA SER LYS SER
SEQRES 4 A 108 LEU ASP ASP VAL LYS LYS ALA PHE TYR VAL 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 SER PRO SER ALA ARG ALA LEU THR
SEQRES 7 A 108 ASP ALA GLU THR LYS ALA PHE LEU ALA ASP GLY ASP LYS
SEQRES 8 A 108 ASP GLY ASP GLY MET ILE GLY VAL ASP GLU PHE ALA ALA
SEQRES 9 A 108 MET ILE LYS ALA
HET ACE A 0 3
HET CA A 110 1
HET CA A 111 1
HET NH4 A 200 1
HETNAM ACE ACETYL GROUP
HETNAM CA CALCIUM ION
HETNAM NH4 AMMONIUM ION
FORMUL 1 ACE C2 H4 O
FORMUL 2 CA 2(CA 2+)
FORMUL 4 NH4 H4 N 1+
FORMUL 5 HOH *72(H2 O)
HELIX 1 A ASP A 8 ALA A 17 1 10
HELIX 2 B HIS A 26 VAL A 33 1 8
HELIX 3 C LEU A 40 ILE A 50 1 11
HELIX 4 D GLU A 60 PHE A 70 1BENDING AT RESIDUE 65 11
HELIX 5 E ASP A 79 GLY A 89 1 11
HELIX 6 F VAL A 99 LYS A 107 1 9
LINK C ACE A 0 N SER A 1 1555 1555 1.33
LINK CA CA A 110 OD1 ASP A 53 1555 1555 2.43
LINK CA CA A 110 OE1 GLU A 59 1555 1555 2.43
LINK CA CA A 110 OE2 GLU A 62 1555 1555 2.62
LINK CA CA A 110 OD1 ASP A 51 1555 1555 2.39
LINK CA CA A 110 OG SER A 55 1555 1555 2.38
LINK CA CA A 110 O PHE A 57 1555 1555 2.32
LINK CA CA A 110 OE1 GLU A 62 1555 1555 2.54
LINK CA CA A 111 OD1 ASP A 92 1555 1555 2.41
LINK CA CA A 111 OD1 ASP A 94 1555 1555 2.43
LINK CA CA A 111 OE1 GLU A 101 1555 1555 2.45
LINK CA CA A 111 OE2 GLU A 101 1555 1555 2.58
LINK CA CA A 111 O HOH A 201 1555 1555 2.41
LINK CA CA A 111 OD1 ASP A 90 1555 1555 2.41
LINK CA CA A 111 O MET A 96 1555 1555 2.33
SITE 1 CD 12 ASP A 51 GLN A 52 ASP A 53 LYS A 54
SITE 2 CD 12 SER A 55 GLY A 56 PHE A 57 ILE A 58
SITE 3 CD 12 GLU A 59 GLU A 60 ASP A 61 GLU A 62
SITE 1 EF 12 ASP A 90 LYS A 91 ASP A 92 GLY A 93
SITE 2 EF 12 ASP A 94 GLY A 95 MET A 96 ILE A 97
SITE 3 EF 12 GLY A 98 VAL A 99 ASP A 100 GLU A 101
SITE 1 AC1 6 ASP A 51 ASP A 53 SER A 55 PHE A 57
SITE 2 AC1 6 GLU A 59 GLU A 62
SITE 1 AC2 6 ASP A 90 ASP A 92 ASP A 94 MET A 96
SITE 2 AC2 6 GLU A 101 HOH A 201
SITE 1 AC3 6 ASP A 53 GLU A 59 ASP A 61 GLU A 62
SITE 2 AC3 6 HOH A 216 HOH A 256
CRYST1 51.840 49.950 34.960 90.00 90.00 90.00 P 21 21 21 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 0.019290 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020020 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028604 0.00000
HETATM 1 C ACE A 0 3.865 17.742 16.631 1.00 7.98 C
HETATM 2 O ACE A 0 3.108 17.293 17.499 1.00 6.91 O
HETATM 3 CH3 ACE A 0 3.484 17.677 15.158 1.00 8.25 C
(ATOM LINES ARE NOT SHOWN.)
END
