HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 07-MAY-07 2Z13
TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DUF1126 IN HUMAN EF-HAND DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: EF-HAND DOMAIN-CONTAINING FAMILY MEMBER C2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 71-190;
COMPND 5 ENGINEERED: YES;
COMPND 6 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: EFHC2;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PX060518-19;
SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS DUF1126, HUMAN EF-HAND, ALTERNATIVE SPLICING, POLYMORPHISM,
KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL
KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS
KEYWDS 4 INITIATIVE, RSGI, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR K.SAITO,S.KISHISHITA,A.NISHINO,K.MURAYAMA,T.TERADA,M.SHIROUZU,
AUTHOR 2 T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE
AUTHOR 3 (RSGI)
REVDAT 3 10-NOV-21 2Z13 1 SEQADV
REVDAT 2 24-FEB-09 2Z13 1 VERSN
REVDAT 1 13-NOV-07 2Z13 0
JRNL AUTH K.SAITO,S.KISHISHITA,A.NISHINO,K.MURAYAMA,T.TERADA,
JRNL AUTH 2 M.SHIROUZU,T.KIGAWA,S.YOKOYAMA
JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DUF1126 IN HUMAN EF-HAND
JRNL TITL 2 DOMAIN
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.84 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.41
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 346110.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.3
REMARK 3 NUMBER OF REFLECTIONS : 10156
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.227
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 507
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008
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) : 1.68
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2270
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 992
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 172
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 7.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.63000
REMARK 3 B22 (A**2) : -0.79000
REMARK 3 B33 (A**2) : -0.84000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.57000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17
REMARK 3 ESD FROM SIGMAA (A) : 0.04
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) : 0.21
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720
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 : FLAT MODEL
REMARK 3 KSOL : 0.38
REMARK 3 BSOL : 48.61
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2Z13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-07.
REMARK 100 THE DEPOSITION ID IS D_1000027387.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-NOV-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL26B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790, 0.9793, 0.964
REMARK 200 MONOCHROMATOR : SI II
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10156
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6
REMARK 200 DATA REDUNDANCY : 3.490
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.03700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.05800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 27.30
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.97
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM IODATE, 0.1M BIS-TRIS, 20%
REMARK 280 PEG3350, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
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 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.73000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.64000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.73000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.64000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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 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 GLY A 1
REMARK 465 SER A 2
REMARK 465 SER A 3
REMARK 465 GLY A 4
REMARK 465 SER A 5
REMARK 465 VAL A 57
REMARK 465 LYS A 58
REMARK 465 ASN A 59
REMARK 465 SER A 60
REMARK 465 GLY A 61
REMARK 465 SER A 128
REMARK 465 GLY A 129
REMARK 465 PRO A 130
REMARK 465 SER A 131
REMARK 465 SER A 132
REMARK 465 GLY A 133
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 ARG A 35 CZ
REMARK 480 CYS A 107 CB
REMARK 480 MET A 118 CE
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 PHE A 11 65.03 -115.84
REMARK 500 LYS A 29 -90.23 72.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: HSI002022525.4 RELATED DB: TARGETDB
DBREF 2Z13 A 8 127 UNP Q5JST6 EFHC2_HUMAN 71 190
SEQADV 2Z13 GLY A 1 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 2 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 3 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 GLY A 4 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 5 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 6 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 GLY A 7 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 MET A 118 UNP Q5JST6 ILE 181 ENGINEERED MUTATION
SEQADV 2Z13 SER A 128 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 GLY A 129 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 PRO A 130 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 131 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 SER A 132 UNP Q5JST6 EXPRESSION TAG
SEQADV 2Z13 GLY A 133 UNP Q5JST6 EXPRESSION TAG
SEQRES 1 A 133 GLY SER SER GLY SER SER GLY TRP VAL ALA PHE ASP LYS
SEQRES 2 A 133 GLN VAL LEU SER PHE ASP ALA TYR LEU GLU GLU GLU VAL
SEQRES 3 A 133 LEU ASP LYS SER GLN THR ASN TYR ARG ILE ARG TYR TYR
SEQRES 4 A 133 LYS ILE TYR PHE TYR PRO GLU ASP ASP THR ILE GLN VAL
SEQRES 5 A 133 ASN GLU PRO GLU VAL LYS ASN SER GLY LEU LEU GLN GLY
SEQRES 6 A 133 THR SER ILE ARG ARG HIS ARG ILE THR LEU PRO PRO PRO
SEQRES 7 A 133 ASP GLU ASP GLN PHE TYR THR VAL TYR HIS PHE ASN VAL
SEQRES 8 A 133 GLY THR GLU VAL VAL PHE TYR GLY ARG THR PHE LYS ILE
SEQRES 9 A 133 TYR ASP CYS ASP ALA PHE THR ARG ASN PHE LEU ARG LYS
SEQRES 10 A 133 MET GLY VAL LYS VAL ASN PRO PRO VAL GLN SER GLY PRO
SEQRES 11 A 133 SER SER GLY
FORMUL 2 HOH *172(H2 O)
HELIX 1 1 THR A 85 PHE A 89 5 5
HELIX 2 2 ASP A 108 MET A 118 1 11
SHEET 1 A 6 SER A 67 HIS A 71 0
SHEET 2 A 6 THR A 49 ASN A 53 -1 N ILE A 50 O HIS A 71
SHEET 3 A 6 GLN A 31 TYR A 44 -1 N TYR A 42 O GLN A 51
SHEET 4 A 6 LEU A 16 ASP A 28 -1 N ASP A 28 O GLN A 31
SHEET 5 A 6 ARG A 100 CYS A 107 -1 O LYS A 103 N TYR A 21
SHEET 6 A 6 GLU A 94 PHE A 97 -1 N VAL A 95 O PHE A 102
CISPEP 1 PRO A 77 PRO A 78 0 0.34
CRYST1 95.460 35.280 39.150 90.00 112.64 90.00 C 1 2 1 4
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 0.010476 0.000000 0.004369 0.00000
SCALE2 0.000000 0.028345 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027675 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
