PDB Short entry for 1J7P 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