HEADER METAL BINDING PROTEIN 17-MAY-01 1J7P
TITLE SOLUTION STRUCTURE OF CALCIUM CALMODULIN C-TERMINAL DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CALMODULIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: AR58
KEYWDS EF HANDS, HELIX BUNDLE, CALCIUM, DIPOLAR COUPLING, METAL BINDING
KEYWDS 2 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 3
AUTHOR J.J.CHOU,C.B.KLEE,A.BAX
REVDAT 4 23-FEB-22 1J7P 1 REMARK LINK
REVDAT 3 24-FEB-09 1J7P 1 VERSN
REVDAT 2 01-APR-03 1J7P 1 JRNL
REVDAT 1 07-NOV-01 1J7P 0
JRNL AUTH J.J.CHOU,S.LI,C.B.KLEE,A.BAX
JRNL TITL SOLUTION STRUCTURE OF CA(2+)-CALMODULIN REVEALS FLEXIBLE
JRNL TITL 2 HAND-LIKE PROPERTIES OF ITS DOMAINS.
JRNL REF NAT.STRUCT.BIOL. V. 8 990 2001
JRNL REFN ISSN 1072-8368
JRNL PMID 11685248
JRNL DOI 10.1038/NSB1101-990
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THIS STRUCTURE IS DETERMINED MAINLY BY RESIDUAL DIPOLAR COUPLINGS
REMARK 3 MEASURED IN A LIQUID CRYSTALLINE PF1 MEDIUM. THE STRUCTURE
REMARK 3 CALCULATION
REMARK 3 SCHEME, DESCRIBED IN THE PAPER, IS BASED ON THE IDEA OF REFINING
REMARK 3 EXISTING
REMARK 3 STRUCTURAL MODELS AGAINST DIPOLAR COUPLINGS TO DERIVE THE CORRECT
REMARK 3 STRUCTURE. HERE A TOTAL OF 305 BACKBONE DIPOLAR COUPLINGS ARE USED
REMARK 3 TO REFINE THE BACKBONE STRUCTURE. ADDITIONALLY, 35 SIDECHAIN
REMARK 3 DIPOLAR COUPLINGS AND 81 3-BOND J COUPLINGS ARE USED TO DETERMINE
REMARK 3 THE SIDECHAIN
REMARK 3 CHI1 AND CHI2 ROTAMERS AS WELL AS THE PRESENCE OF ROTAMERIC
REMARK 3 AVERAGING. A
REMARK 3 TOTAL OF THREE STRUCTURES (MODEL 1-3) WERE CALCULATED STARTING
REMARK 3 FROM THE 1. A CRYSTAL STRUCTURE OF CA-CALMODULIN (PDB ENTRY 1EXR),
REMARK 3 THE NMR STRUCTURE
REMARK 3 OF APO-CALMODULIN (1F70), AND THE CRYSTAL STRUCTURE OF CA-LIGATED
REMARK 3 PARVALBUMIN (1CDP). THE CONVERGENCE OF REFINEMENT IS
REMARK 3 INDICATED BY THE SMALL AVERAGE RMSD BETWEEN THE THREE CALCULATED
REMARK 3 STRUCTURES AND THE AVERAGE COORDINATES (0.26 A FOR BACKBONE AND
REMARK 3 0.90 FOR
REMARK 3 ALL HEAVY ATOMS). DURING THE THREE-STAGE SIMULATED ANNEALING
REMARK 3 DESCRIBED IN
REMARK 3 THE PAPER, RESTRAINTS ARE INCLUDED FOR MOST PREVIOUSLY ESTABLISHED
REMARK 3 HYDROGEN BONDS, BUT HAVE ONLY MINUTE EFFECTS (< 0.3 A) ON THE
REMARK 3 FINAL STRUCTURE.
REMARK 4
REMARK 4 1J7P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-01.
REMARK 100 THE DEPOSITION ID IS D_1000013463.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 305; 305; 305
REMARK 210 PH : 7.0; 7.0; 7.0
REMARK 210 IONIC STRENGTH : 100MM KCL; 10MM KCL; 100MM KCL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM CALMODULIN U-15N,13C; 100MM
REMARK 210 KCL, 16MM CACL2, PH 7.0;; 1MM
REMARK 210 CALMODULIN U-15N,13C; 10MM KCL,
REMARK 210 16MM CACL2, PH 7.0; 15 MG/ML PF1;
REMARK 210 ; 0.5MM CALMODULIN U-15N,13C;
REMARK 210 100MM KCL, 6MM CACL2, PH 7.0; 18
REMARK 210 MG/ML PF1;
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO (NH COUPLED); 3D HNCO
REMARK 210 (C'CA COUPLED); CBCA(CO)NH
REMARK 210 (QUANTITATIVE J); TROSY HNCO
REMARK 210 (QUANTITATIVE J); HNCOCA (C'HA
REMARK 210 COUPLED); 3D 13C-SEPARATED NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.0
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 3
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 3
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE WITH THE LOWEST
REMARK 210 DIPOLAR ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2
REMARK 210
REMARK 210 REMARK:
REMARK 210 A TOTAL OF FIVE SETS OF DIPOLAR COUPLINGS ARE MEASURED, INCLUDING
REMARK 210 THE ONE-BOND NH, CAHA, C'CA, AND NC' COUPLINGS, AND THE TWO-BOND C'
REMARK 210 HA COUPLINGS.
REMARK 210 ADDITIONALLY, THE CBHB DIPOLAR COUPLINGS WERE MEASURE TO ASSIGN
REMARK 210 CHI-1 ROTAMERS FOR LOCKED SIDECHAINS.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-3
REMARK 470 RES CSSEQI ATOMS
REMARK 470 TYR A 99 OH
REMARK 470 TYR A 138 OH
REMARK 470 LYS A 148 O
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OD2 ASP A 93 H GLY A 98 1.44
REMARK 500 OD2 ASP A 129 H GLY A 134 1.45
REMARK 500 OD1 ASP A 131 H ASP A 133 1.56
REMARK 500 OD1 ASP A 95 H ASN A 97 1.56
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 1 ALA A 147 91.97 -54.69
REMARK 500 2 ALA A 147 -140.64 46.86
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 A1000 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 93 OD1
REMARK 620 2 ASP A 95 OD1 52.5
REMARK 620 3 ASP A 95 OD2 97.4 46.9
REMARK 620 4 ASN A 97 ND2 99.9 77.0 78.6
REMARK 620 5 ASN A 97 OD1 54.4 61.9 97.7 47.5
REMARK 620 6 TYR A 99 O 90.5 121.3 144.2 65.6 59.5
REMARK 620 7 GLU A 104 OE1 120.3 153.0 121.8 128.5 139.8 82.2
REMARK 620 8 GLU A 104 OE2 111.6 106.0 77.5 142.4 164.9 131.3 49.2
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1001 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 129 OD1
REMARK 620 2 ASP A 131 OD2 95.6
REMARK 620 3 ASP A 131 OD1 51.9 46.8
REMARK 620 4 ASP A 133 OD1 58.7 96.1 60.9
REMARK 620 5 ASP A 133 OD2 103.3 80.0 78.2 46.2
REMARK 620 6 GLN A 135 O 87.5 156.4 124.1 65.6 76.5
REMARK 620 7 ASN A 137 ND2 150.2 84.3 130.2 151.0 106.0 104.4
REMARK 620 8 GLU A 140 OE2 79.7 85.6 93.3 138.4 165.5 118.0 70.6
REMARK 620 9 GLU A 140 OE1 93.9 130.9 136.1 129.3 143.2 72.0 65.2 49.2
REMARK 620 N 1 2 3 4 5 6 7 8
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 1000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1F71 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF APO CALMODULIN C-TERMINAL DOMAIN
REMARK 900 RELATED ID: 1EXR RELATED DB: PDB
REMARK 900 1 A CRYSTAL STRUCTURE OF CALCIUM CALMODULIN (PARAMECIUM)
REMARK 900 RELATED ID: 1CLL RELATED DB: PDB
REMARK 900 1.7 A CRYSTAL STRUCTURE OF CALCIUM LIGATED HUMAN CALMODULIN
DBREF 1J7P A 82 148 UNP P62158 CALM_HUMAN 82 148
SEQRES 1 A 67 GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL PHE ASP LYS
SEQRES 2 A 67 ASP GLY ASN GLY TYR ILE SER ALA ALA GLU LEU ARG HIS
SEQRES 3 A 67 VAL MET THR ASN LEU GLY GLU LYS LEU THR ASP GLU GLU
SEQRES 4 A 67 VAL ASP GLU MET ILE ARG GLU ALA ASP ILE ASP GLY ASP
SEQRES 5 A 67 GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN MET MET THR
SEQRES 6 A 67 ALA LYS
HET CA A1000 1
HET CA A1001 1
HETNAM CA CALCIUM ION
FORMUL 2 CA 2(CA 2+)
HELIX 1 1 GLU A 82 ASP A 93 1 12
HELIX 2 2 SER A 101 LEU A 112 1 12
HELIX 3 3 THR A 117 ASP A 129 1 13
HELIX 4 4 TYR A 138 THR A 146 1 9
SHEET 1 A 2 TYR A 99 ILE A 100 0
SHEET 2 A 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE A 100
LINK OD1 ASP A 93 CA CA A1000 1555 1555 2.59
LINK OD1 ASP A 95 CA CA A1000 1555 1555 2.80
LINK OD2 ASP A 95 CA CA A1000 1555 1555 2.60
LINK ND2 ASN A 97 CA CA A1000 1555 1555 2.81
LINK OD1 ASN A 97 CA CA A1000 1555 1555 2.59
LINK O TYR A 99 CA CA A1000 1555 1555 2.59
LINK OE1 GLU A 104 CA CA A1000 1555 1555 2.59
LINK OE2 GLU A 104 CA CA A1000 1555 1555 2.58
LINK OD1 ASP A 129 CA CA A1001 1555 1555 2.59
LINK OD2 ASP A 131 CA CA A1001 1555 1555 2.59
LINK OD1 ASP A 131 CA CA A1001 1555 1555 2.81
LINK OD1 ASP A 133 CA CA A1001 1555 1555 2.59
LINK OD2 ASP A 133 CA CA A1001 1555 1555 2.86
LINK O GLN A 135 CA CA A1001 1555 1555 2.60
LINK ND2 ASN A 137 CA CA A1001 1555 1555 2.68
LINK OE2 GLU A 140 CA CA A1001 1555 1555 2.59
LINK OE1 GLU A 140 CA CA A1001 1555 1555 2.58
SITE 1 AC1 5 ASP A 93 ASP A 95 ASN A 97 TYR A 99
SITE 2 AC1 5 GLU A 104
SITE 1 AC2 6 ASP A 129 ASP A 131 ASP A 133 GLN A 135
SITE 2 AC2 6 ASN A 137 GLU A 140
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END