HEADER SIGNALING PROTEIN 17-SEP-15 5DSU TITLE CRYSTAL STRUCTURE OF DOUBLE MUTANT OF N-DOMAIN OF HUMAN CALMODULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 3-78; COMPND 5 SYNONYM: CAM; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, SOURCE 6 CAM3, CAMC, CAMIII; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS CA2+ BINDING PROTEIN EF-HAND DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ABABOU,M.ZALESKA REVDAT 4 10-JAN-24 5DSU 1 REMARK REVDAT 3 12-APR-17 5DSU 1 JRNL REVDAT 2 05-APR-17 5DSU 1 JRNL REVDAT 1 11-JAN-17 5DSU 0 JRNL AUTH A.ABABOU,M.ZALESKA,M.PFUHL JRNL TITL ON THE CA(2+) BINDING AND CONFORMATIONAL CHANGE IN EF-HAND JRNL TITL 2 DOMAINS: EXPERIMENTAL EVIDENCE OF CA(2+)-SATURATED JRNL TITL 3 INTERMEDIATES OF N-DOMAIN OF CALMODULIN. JRNL REF BIOCHIM. BIOPHYS. ACTA V.1865 640 2017 JRNL REFN ISSN 0006-3002 JRNL PMID 28288938 JRNL DOI 10.1016/J.BBAPAP.2017.03.003 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 252 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.9936 - 2.4310 0.99 2709 133 0.2179 0.2413 REMARK 3 2 2.4310 - 1.9300 0.99 2583 119 0.2619 0.3478 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 599 REMARK 3 ANGLE : 1.312 800 REMARK 3 CHIRALITY : 0.084 91 REMARK 3 PLANARITY : 0.004 105 REMARK 3 DIHEDRAL : 18.653 231 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DSU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5544 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.992 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1CLL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37% PEG 400, 100 MM HEPES, 250 MM REMARK 280 CACL2, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.13333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.06667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.06667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.13333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 TYR A 78 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 203 O HOH A 226 2444 2.18 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 A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 22 OD1 79.8 REMARK 620 3 ASP A 24 OD1 99.9 81.4 REMARK 620 4 THR A 26 O 88.9 163.6 88.9 REMARK 620 5 GLU A 31 OE1 81.7 70.2 150.9 120.2 REMARK 620 6 GLU A 31 OE2 99.2 115.5 156.5 77.9 46.5 REMARK 620 7 HOH A 211 O 160.0 82.8 87.1 110.1 83.2 79.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 ASP A 58 OD1 83.0 REMARK 620 3 ASN A 60 OD1 89.4 76.5 REMARK 620 4 THR A 62 O 92.7 155.1 79.0 REMARK 620 5 GLU A 67 OE1 105.2 126.7 153.3 78.1 REMARK 620 6 GLU A 67 OE2 92.3 77.3 153.4 127.4 50.2 REMARK 620 7 HOH A 237 O 167.2 101.0 79.8 78.6 82.3 100.4 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 103 DBREF 5DSU A 2 77 UNP P62158 CALM_HUMAN 3 78 SEQADV 5DSU MET A 1 UNP P62158 INITIATING METHIONINE SEQADV 5DSU TYR A 19 UNP P62158 PHE 20 ENGINEERED MUTATION SEQADV 5DSU LEU A 41 UNP P62158 GLN 42 ENGINEERED MUTATION SEQADV 5DSU ILE A 75 UNP P62158 LYS 76 ENGINEERED MUTATION SEQADV 5DSU TYR A 78 UNP P62158 EXPRESSION TAG SEQRES 1 A 78 MET ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 78 GLU ALA PHE SER LEU TYR ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 78 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 78 GLY LEU ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 78 ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 78 PRO GLU PHE LEU THR MET MET ALA ARG ILE MET LYS TYR HET CA A 101 1 HET CA A 102 1 HET PGE A 103 10 HETNAM CA CALCIUM ION HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 CA 2(CA 2+) FORMUL 4 PGE C6 H14 O4 FORMUL 5 HOH *56(H2 O) HELIX 1 AA1 THR A 5 ASP A 20 1 16 HELIX 2 AA2 THR A 28 LEU A 39 1 12 HELIX 3 AA3 THR A 44 ASP A 56 1 13 HELIX 4 AA4 ASP A 64 LYS A 77 1 14 LINK OD1 ASP A 20 CA CA A 101 1555 1555 2.16 LINK OD1 ASP A 22 CA CA A 101 1555 1555 2.51 LINK OD1 ASP A 24 CA CA A 101 1555 1555 2.33 LINK O THR A 26 CA CA A 101 1555 1555 2.33 LINK OE1 GLU A 31 CA CA A 101 1555 1555 2.84 LINK OE2 GLU A 31 CA CA A 101 1555 1555 2.71 LINK OD1 ASP A 56 CA CA A 102 1555 1555 2.28 LINK OD1 ASP A 58 CA CA A 102 1555 1555 2.51 LINK OD1 ASN A 60 CA CA A 102 1555 1555 2.30 LINK O THR A 62 CA CA A 102 1555 1555 2.38 LINK OE1 GLU A 67 CA CA A 102 1555 1555 2.56 LINK OE2 GLU A 67 CA CA A 102 1555 1555 2.63 LINK CA CA A 101 O HOH A 211 1555 1555 2.28 LINK CA CA A 102 O HOH A 237 1555 1555 2.66 SITE 1 AC1 6 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 6 GLU A 31 HOH A 211 SITE 1 AC2 6 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 6 GLU A 67 HOH A 237 SITE 1 AC3 4 TYR A 19 LEU A 39 MET A 72 ILE A 75 CRYST1 38.400 38.400 81.200 90.00 90.00 120.00 P 32 2 1 6 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 0.026042 0.015035 0.000000 0.00000 SCALE2 0.000000 0.030070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012315 0.00000