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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END