HEADER METAL BINDING PROTEIN 01-MAY-07 2PQ3 TITLE N-TERMINAL CALMODULIN ZN-TRAPPED INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAM; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: CALM1, CALM, CAM, CAM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-PUBS520; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPRO-EX KEYWDS CALMODULIN, HELIX-TURN-HELIX, EF-HAND, N-TERMINAL CALMODULIN, CAM, N- KEYWDS 2 CAM, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.T.WARREN,Q.GUO,W.J.TANG REVDAT 5 21-FEB-24 2PQ3 1 REMARK REVDAT 4 13-JUL-11 2PQ3 1 VERSN REVDAT 3 24-FEB-09 2PQ3 1 VERSN REVDAT 2 22-JAN-08 2PQ3 1 JRNL REVDAT 1 16-OCT-07 2PQ3 0 JRNL AUTH J.T.WARREN,Q.GUO,W.J.TANG JRNL TITL A 1.3-A STRUCTURE OF ZINC-BOUND N-TERMINAL DOMAIN OF JRNL TITL 2 CALMODULIN ELUCIDATES POTENTIAL EARLY ION-BINDING STEP. JRNL REF J.MOL.BIOL. V. 374 517 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17942116 JRNL DOI 10.1016/J.JMB.2007.09.048 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 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) : 0.143 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.143 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 634 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12815 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.136 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 18450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 575 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 711.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 7.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7049 REMARK 3 NUMBER OF RESTRAINTS : 9042 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.058 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.075 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.019 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.104 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792911 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA CACODYLATE, 5MM ZN ACETATE, REMARK 280 16% PEG8000, PH 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.64700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 17.60550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 17.60550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.47050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 17.60550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 17.60550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.82350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 17.60550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 17.60550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.47050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 17.60550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 17.60550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.82350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.64700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 ASP A 2 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 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 22 OD2 REMARK 620 2 ASP A 24 OD2 106.5 REMARK 620 3 CAC A 200 O2 111.9 99.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 64 OD2 REMARK 620 2 GLU A 67 OE2 110.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 DBREF 2PQ3 A 1 76 UNP P62161 CALM_RAT 2 77 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 CAC A 200 5 HET ZN A 201 2 HET ZN A 202 1 HETNAM CAC CACODYLATE ION HETNAM ZN ZINC ION HETSYN CAC DIMETHYLARSINATE FORMUL 2 CAC C2 H6 AS O2 1- FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *129(H2 O) HELIX 1 1 THR A 5 PHE A 19 1 15 HELIX 2 2 GLU A 31 LEU A 39 1 9 HELIX 3 3 THR A 44 ASP A 56 1 13 HELIX 4 4 PHE A 65 MET A 76 1 12 SHEET 1 A 2 THR A 26 THR A 28 0 SHEET 2 A 2 THR A 62 ASP A 64 -1 O ILE A 63 N ILE A 27 LINK OD2 ASP A 22 ZN ZN A 202 1555 1555 2.00 LINK OD2 ASP A 24 ZN ZN A 202 1555 1555 1.93 LINK OD2 ASP A 64 ZN A ZN A 201 1555 1555 2.06 LINK OE2 GLU A 67 ZN A ZN A 201 1555 1555 1.82 LINK O2 CAC A 200 ZN ZN A 202 1555 1555 1.97 SITE 1 AC1 7 ASP A 22 ASP A 24 THR A 26 ILE A 27 SITE 2 AC1 7 ZN A 202 HOH A 206 HOH A 228 SITE 1 AC2 4 GLU A 7 GLU A 11 ASP A 64 GLU A 67 SITE 1 AC3 3 ASP A 22 ASP A 24 CAC A 200 CRYST1 35.211 35.211 143.294 90.00 90.00 90.00 P 43 21 2 8 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 0.028400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006979 0.00000