HEADER METAL BINDING PROTEIN 10-AUG-06 2I08
TITLE SOLVATION EFFECT IN CONFORMATIONAL CHANGES OF EF-HAND PROTEINS: X-RAY
TITLE 2 STRUCTURE OF CA2+-SATURATED DOUBLE MUTANT Q41L-K75I OF N-DOMAIN OF
TITLE 3 CALMODULIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CALMODULIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: N-DOMAIN OF CALMODULIN;
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 STRAIN: HUMAN;
SOURCE 6 GENE: CALM1;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET3A
KEYWDS CALMODULIN, EF-HAND, CALCIUM-BINDING PROTEIN, CONFORMATIONAL CHANGE,
KEYWDS 2 METAL BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR A.ABABOU,G.N.PARKINSON,J.R.DESJARLAIS,S.DJORDJEVIC
REVDAT 5 30-AUG-23 2I08 1 REMARK
REVDAT 4 20-OCT-21 2I08 1 REMARK SEQADV
REVDAT 3 13-JUL-11 2I08 1 VERSN
REVDAT 2 24-FEB-09 2I08 1 VERSN
REVDAT 1 21-AUG-07 2I08 0
JRNL AUTH A.ABABOU,G.N.PARKINSON,J.R.DESJARLAIS,S.DJORDJEVIC
JRNL TITL SOLVATION EFFECT IN CONFORMATIONAL CHANGES OF EF-HAND
JRNL TITL 2 PROTEINS: X-RAY STRUCTURE OF DOUBLE MUTANT Q41L-K75I OF
JRNL TITL 3 N-DOMAIN OF CALMODULIN
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.73
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 880706.930
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5
REMARK 3 NUMBER OF REFLECTIONS : 4811
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.239
REMARK 3 FREE R VALUE : 0.243
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 238
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.80
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 663
REMARK 3 BIN R VALUE (WORKING SET) : 0.2660
REMARK 3 BIN FREE R VALUE : 0.3220
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.056
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 574
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 8
REMARK 3 SOLVENT ATOMS : 50
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 21.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.20000
REMARK 3 B22 (A**2) : -0.20000
REMARK 3 B33 (A**2) : 0.41000
REMARK 3 B12 (A**2) : 1.30000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27
REMARK 3 ESD FROM SIGMAA (A) : 0.18
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.014
REMARK 3 BOND ANGLES (DEGREES) : 1.600
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : 0.37
REMARK 3 BSOL : 71.72
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : CNS_GLY_PARAM.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : CNS_GLY_TOP.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2I08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-06.
REMARK 100 THE DEPOSITION ID IS D_1000038973.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-OCT-01
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS MSC, OREM
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR
REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5553
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 79.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: EPMR
REMARK 200 STARTING MODEL: PDB ENTRY 1CLL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.41
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 36% (V/V) PEG 400, 100 MM HEPES, 200
REMARK 280 MM CACL2, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
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 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 LYS A 77
REMARK 465 TYR A 78
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 200 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 20 OD1
REMARK 620 2 ASP A 22 OD1 79.2
REMARK 620 3 ASP A 24 OD1 91.9 75.9
REMARK 620 4 THR A 26 O 87.3 154.5 83.2
REMARK 620 5 GLU A 31 OE1 89.3 76.8 152.0 124.8
REMARK 620 6 GLU A 31 OE2 101.8 127.1 154.8 76.6 50.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 201 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 56 OD1
REMARK 620 2 ASP A 58 OD1 77.5
REMARK 620 3 ASN A 60 OD1 88.0 73.7
REMARK 620 4 THR A 62 O 92.5 149.0 76.7
REMARK 620 5 GLU A 67 OE1 109.3 128.3 153.7 82.7
REMARK 620 6 GLU A 67 OE2 90.9 76.5 149.7 133.6 52.8
REMARK 620 7 HOH A 208 O 165.9 89.1 84.0 96.9 82.4 90.2
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 200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 100
DBREF 2I08 A 1 78 UNP P62155 CALM_XENLA 1 78
SEQADV 2I08 MET A 1 UNP P62155 ALA 1 ENGINEERED MUTATION
SEQADV 2I08 TYR A 19 UNP P62155 PHE 19 ENGINEERED MUTATION
SEQADV 2I08 LEU A 41 UNP P62155 GLN 41 ENGINEERED MUTATION
SEQADV 2I08 ILE A 75 UNP P62155 LYS 75 ENGINEERED MUTATION
SEQADV 2I08 TYR A 78 UNP P62155 ASP 78 ENGINEERED MUTATION
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 200 1
HET CA A 201 1
HET GOL A 100 6
HETNAM CA CALCIUM ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 CA 2(CA 2+)
FORMUL 4 GOL C3 H8 O3
FORMUL 5 HOH *50(H2 O)
HELIX 1 1 THR A 5 ASP A 20 1 16
HELIX 2 2 THR A 28 GLY A 40 1 13
HELIX 3 3 THR A 44 ASP A 56 1 13
HELIX 4 4 ASP A 64 MET A 76 1 13
LINK OD1 ASP A 20 CA CA A 200 1555 1555 2.06
LINK OD1 ASP A 22 CA CA A 200 1555 1555 2.64
LINK OD1 ASP A 24 CA CA A 200 1555 1555 2.50
LINK O THR A 26 CA CA A 200 1555 1555 2.36
LINK OE1 GLU A 31 CA CA A 200 1555 1555 2.57
LINK OE2 GLU A 31 CA CA A 200 1555 1555 2.59
LINK OD1 ASP A 56 CA CA A 201 1555 1555 2.39
LINK OD1 ASP A 58 CA CA A 201 1555 1555 2.55
LINK OD1 ASN A 60 CA CA A 201 1555 1555 2.44
LINK O THR A 62 CA CA A 201 1555 1555 2.38
LINK OE1 GLU A 67 CA CA A 201 1555 1555 2.40
LINK OE2 GLU A 67 CA CA A 201 1555 1555 2.53
LINK CA CA A 201 O HOH A 208 1555 1555 2.66
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 6 ASP A 56 ASP A 58 ASN A 60 THR A 62
SITE 2 AC2 6 GLU A 67 HOH A 208
SITE 1 AC3 5 GLU A 7 ASN A 42 PRO A 43 THR A 44
SITE 2 AC3 5 GLU A 47
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