PDB Short entry for 1J7O HEADER METAL BINDING PROTEIN 17-MAY-01 1J7O TITLE SOLUTION STRUCTURE OF CALCIUM-CALMODULIN N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-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, CALCIUM BINDING, HELIX BUNDLE, MINI BETA STRAND, METAL KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 3 AUTHOR J.J.CHOU,C.B.KLEE,A.BAX REVDAT 4 23-FEB-22 1J7O 1 REMARK LINK REVDAT 3 24-FEB-09 1J7O 1 VERSN REVDAT 2 01-APR-03 1J7O 1 JRNL REVDAT 1 07-NOV-01 1J7O 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 SCHEME, DESCRIBED IN THE PAPER, IS BASED ON THE IDEA REMARK 3 OF REFINING EXISTING REMARK 3 STRUCTURAL MODELS AGAINST DIPOLAR COUPLINGS TO DERIVE THECORRECT REMARK 3 STRUCTURE. HERE A TOTAL OF 323 BACKBONE DIPOLAR COUPLINGS ARE USED REMARK 3 TO REFINE THE BACKBONE STRUCTURE. ADDITIONALLY, 38 SIDECHAIN REMARK 3 DIPOLAR REMARK 3 COUPLINGS AND 85 3-BOND J COUPLINGS ARE USED TO DETERMINE THE REMARK 3 SIDECHAIN REMARK 3 CHI1 AND CHI2 ROTAMERS AS WELL AS THE PRESENCE OF ROTAMERIC REMARK 3 AVERAGING. A TOTAL OF THREE STRUCTURES (MODEL 1-3) WERE CALCULATED REMARK 3 STARTING FROM THE 1. REMARK 3 A CRYSTAL STRUCTURE OF CA-CALMODULIN (PDB ENTRY 1EXR), THE NMR REMARK 3 STRUCTURE OF APO-CALMODULIN (1F70), AND THE CRYSTAL STRUCTURE OF REMARK 3 CA-LIGATED 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 REMARK 3 COORDINATES (0.28 A FOR BACKBONE AND 0.87 FOR ALL HEAVY ATOMS). REMARK 3 DURING THE THREE-STAGE SIMULATED ANNEALING DESCRIBED IN THE PAPER, REMARK 3 RESTRAINTS ARE INCLUDED FOR MOST PREVIOUSLY ESTABLISHED HYDROGEN REMARK 3 BONDS, REMARK 3 BUT HAVE ONLY MINUTE EFFECTS (< 0.3 A) ON THE FINAL STRUCTURE. REMARK 4 REMARK 4 1J7O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013462. 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 (COCA COUPLED); CBCA(CO)NH REMARK 210 (QUANTITATIVE J); HNCOCA (COHA REMARK 210 COUPLED); 3D TROSY-HNCO REMARK 210 (QUANTITATIVE J); 3D 13C- REMARK 210 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 LOWEST DIPOLAR REMARK 210 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 SIDECHAIN CBHB DIPOLAR COUPLINGS ARE MEASURED TO REMARK 210 ASSIGN 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 MET A 76 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 OD1 ASN A 60 H THR A 62 1.45 REMARK 500 OD1 ASP A 22 H ASP A 24 1.46 REMARK 500 OD1 ASP A 58 H ASN A 60 1.52 REMARK 500 OD2 ASP A 56 H GLY A 61 1.52 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 ASP A 2 -75.00 -65.89 REMARK 500 1 GLN A 3 -96.92 -90.48 REMARK 500 1 ASP A 64 -152.36 -103.00 REMARK 500 2 ASP A 64 -150.43 -126.53 REMARK 500 3 ASP A 64 -150.15 -124.75 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 20 OD1 REMARK 620 2 ASP A 22 OD1 53.7 REMARK 620 3 ASP A 22 OD2 98.4 48.7 REMARK 620 4 ASP A 24 OD1 79.0 54.1 76.0 REMARK 620 5 THR A 26 O 139.0 128.6 108.0 77.6 REMARK 620 6 GLU A 31 OE1 112.8 136.8 106.2 167.1 89.7 REMARK 620 7 GLU A 31 OE2 106.2 92.0 58.6 134.6 114.2 49.2 REMARK 620 N 1 2 3 4 5 6 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 56 OD2 REMARK 620 2 ASP A 58 OD1 75.8 REMARK 620 3 ASP A 58 OD2 114.0 44.6 REMARK 620 4 ASN A 60 OD1 54.4 74.7 80.7 REMARK 620 5 THR A 62 O 86.9 136.7 115.2 63.1 REMARK 620 6 GLU A 67 OE1 151.0 130.3 87.1 114.5 65.5 REMARK 620 7 GLU A 67 OE2 160.1 85.5 52.8 127.1 111.8 48.8 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 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: 1F70 RELATED DB: PDB REMARK 900 1F70 IS THE CALCIUM-FREE CALMODULIN N-TERMINAL DOMAIN. IT IS IN THE REMARK 900 CLOSED FORM. REMARK 900 RELATED ID: 1EXR RELATED DB: PDB REMARK 900 THE 1 A CRYSTAL STRUCTURE OF CALCIUM-CALMODULIN. THIS IS THE REMARK 900 PARAMECIUM CALMODULIN. REMARK 900 RELATED ID: 1CLL RELATED DB: PDB REMARK 900 THE 1.7 A CRYSTAL STRUCTURE OF HUMAN CALMODULIN BOUND TO CALCIUM. DBREF 1J7O A 1 76 UNP P62158 CALM_HUMAN 1 76 SEQRES 1 A 76 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 76 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 76 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 76 GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 76 ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 76 PRO GLU PHE LEU THR MET MET ALA ARG LYS MET HET CA A1000 1 HET CA A1001 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 THR A 5 ASP A 20 1 16 HELIX 2 2 THR A 28 LEU A 39 1 12 HELIX 3 3 THR A 44 GLU A 54 1 11 HELIX 4 4 ASP A 64 MET A 76 1 13 LINK OD1 ASP A 20 CA CA A1000 1555 1555 2.59 LINK OD1 ASP A 22 CA CA A1000 1555 1555 2.64 LINK OD2 ASP A 22 CA CA A1000 1555 1555 2.59 LINK OD1 ASP A 24 CA CA A1000 1555 1555 2.59 LINK O THR A 26 CA CA A1000 1555 1555 2.59 LINK OE1 GLU A 31 CA CA A1000 1555 1555 2.59 LINK OE2 GLU A 31 CA CA A1000 1555 1555 2.59 LINK OD2 ASP A 56 CA CA A1001 1555 1555 2.59 LINK OD1 ASP A 58 CA CA A1001 1555 1555 2.58 LINK OD2 ASP A 58 CA CA A1001 1555 1555 3.00 LINK OD1 ASN A 60 CA CA A1001 1555 1555 2.58 LINK O THR A 62 CA CA A1001 1555 1555 2.58 LINK OE1 GLU A 67 CA CA A1001 1555 1555 2.60 LINK OE2 GLU A 67 CA CA A1001 1555 1555 2.60 SITE 1 AC1 5 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 5 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 5 GLU A 67 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