HEADER TRANSFERASE 21-OCT-03 1R79
TITLE SOLUTION STRUCTURE OF THE C1 DOMAIN OF THE HUMAN DIACYLGLYCEROL KINASE
TITLE 2 DELTA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIACYLGLYCEROL KINASE, DELTA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C1 DOMAIN;
COMPND 5 SYNONYM: DIGLYCERIDE KINASE, DGK-DELTA, DAG KINASE DELTA, 130 KDA
COMPND 6 DIACYLGLYCEROL KINASE, DIACYLGLYCEROL KINASE DELTA(KIAA0145);
COMPND 7 EC: 2.7.1.107;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: KAZUSA CDNA HA00914;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P030128-49;
SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS C1 DOMAIN, CYSTEIN-RICH ZINC BINDING DOMAIN, DIACYLGLYCEROL KINASE
KEYWDS 2 DELTA, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS
KEYWDS 3 INITIATIVE, RSGI, TRANSFERASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR K.MIYAMOTO,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN
AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 02-MAR-22 1R79 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1R79 1 VERSN
REVDAT 1 21-APR-04 1R79 0
JRNL AUTH K.MIYAMOTO,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA
JRNL TITL SOLUTION STRUCTURE OF THE C1 DOMAIN OF THE HUMAN
JRNL TITL 2 DIACYLGLYCEROL KINASE DELTA
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17
REMARK 3 AUTHORS : BRUKER (XWINNMR), GUENTERT, P (CYANA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1R79 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-03.
REMARK 100 THE DEPOSITION ID IS D_1000020523.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.5
REMARK 210 IONIC STRENGTH : 120MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.05MM C1 DOMAIN U-15N, 13C;
REMARK 210 20MM D-TRIS-HCL(PH 7.5); 100MM
REMARK 210 NACL; 0.02% NAN3; 100UM ZNCL2;
REMARK 210 90% H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5.0.4,
REMARK 210 KUJIRA 0.863, CYANA 2.0.17
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY, TARGET
REMARK 210 FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 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 1 SER A 5 142.59 -173.73
REMARK 500 1 SER A 6 149.64 -171.83
REMARK 500 1 ASP A 22 -50.11 -131.05
REMARK 500 1 ILE A 24 138.88 -32.48
REMARK 500 1 PRO A 27 -170.74 -69.79
REMARK 500 1 SER A 38 40.93 -103.52
REMARK 500 1 ARG A 53 -31.49 -132.56
REMARK 500 1 ASP A 56 141.28 -32.40
REMARK 500 1 THR A 76 148.62 -32.99
REMARK 500 1 SER A 82 145.79 -174.81
REMARK 500 1 SER A 83 -58.62 -129.05
REMARK 500 2 THR A 9 111.08 -160.61
REMARK 500 2 LEU A 10 -63.73 -101.63
REMARK 500 2 ASP A 16 108.96 -166.23
REMARK 500 2 ILE A 17 113.68 -35.91
REMARK 500 2 PRO A 27 -178.71 -69.78
REMARK 500 2 THR A 47 119.83 -35.87
REMARK 500 2 SER A 50 125.31 -38.04
REMARK 500 2 ARG A 53 141.78 -173.07
REMARK 500 2 ASP A 56 161.07 -41.14
REMARK 500 2 TRP A 61 -71.65 -108.35
REMARK 500 2 THR A 76 158.04 -42.33
REMARK 500 3 ASP A 20 -175.41 -54.85
REMARK 500 3 ASP A 22 116.64 -166.84
REMARK 500 3 PRO A 27 -179.15 -69.81
REMARK 500 3 ASN A 34 31.81 73.61
REMARK 500 3 THR A 47 144.98 -32.21
REMARK 500 3 ARG A 53 149.42 -170.92
REMARK 500 3 LEU A 54 96.82 -53.88
REMARK 500 3 ASP A 56 154.61 -36.21
REMARK 500 3 TRP A 61 -70.89 -93.56
REMARK 500 3 THR A 68 -37.09 -34.59
REMARK 500 4 SER A 2 141.02 -171.77
REMARK 500 4 THR A 8 168.59 -44.71
REMARK 500 4 LEU A 10 45.80 34.62
REMARK 500 4 ILE A 17 115.11 -36.25
REMARK 500 4 ASP A 20 172.24 -55.79
REMARK 500 4 PRO A 27 -169.85 -69.83
REMARK 500 4 GLU A 32 138.35 -34.15
REMARK 500 4 SER A 38 38.87 -93.79
REMARK 500 4 ASP A 45 44.30 75.02
REMARK 500 4 THR A 47 145.02 -35.86
REMARK 500 4 LEU A 54 125.58 -34.41
REMARK 500 4 GLN A 55 -41.81 -130.51
REMARK 500 4 ASP A 56 152.59 -35.12
REMARK 500 4 TRP A 61 -73.40 -91.81
REMARK 500 4 THR A 76 131.88 -33.75
REMARK 500 4 PRO A 81 0.12 -69.77
REMARK 500 5 SER A 3 -58.10 -122.53
REMARK 500 5 SER A 6 42.40 -81.80
REMARK 500
REMARK 500 THIS ENTRY HAS 234 RAMACHANDRAN OUTLIERS.
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 ZN A 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 28 ND1
REMARK 620 2 CYS A 59 SG 115.4
REMARK 620 3 CYS A 62 SG 106.7 103.5
REMARK 620 4 CYS A 78 SG 101.1 112.1 118.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 401 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 41 SG
REMARK 620 2 CYS A 44 SG 98.4
REMARK 620 3 HIS A 67 ND1 104.8 108.0
REMARK 620 4 CYS A 70 SG 118.7 109.1 116.1
REMARK 620 N 1 2 3
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: HSK002000142.1 RELATED DB: TARGETDB
DBREF 1R79 A 8 78 UNP Q16760 DGKD_HUMAN 197 267
SEQADV 1R79 GLY A 1 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 2 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 3 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 GLY A 4 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 5 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 6 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 GLY A 7 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 79 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 GLY A 80 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 PRO A 81 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 82 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 SER A 83 UNP Q16760 CLONING ARTIFACT
SEQADV 1R79 GLY A 84 UNP Q16760 CLONING ARTIFACT
SEQRES 1 A 84 GLY SER SER GLY SER SER GLY THR THR LEU ALA SER ILE
SEQRES 2 A 84 GLY LYS ASP ILE ILE GLU ASP ALA ASP GLY ILE ALA MET
SEQRES 3 A 84 PRO HIS GLN TRP LEU GLU GLY ASN LEU PRO VAL SER ALA
SEQRES 4 A 84 LYS CYS THR VAL CYS ASP LYS THR CYS GLY SER VAL LEU
SEQRES 5 A 84 ARG LEU GLN ASP TRP ARG CYS LEU TRP CYS LYS ALA MET
SEQRES 6 A 84 VAL HIS THR SER CYS LYS GLU SER LEU LEU THR LYS CYS
SEQRES 7 A 84 SER GLY PRO SER SER GLY
HET ZN A 201 1
HET ZN A 401 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 THR A 68 SER A 73 1 6
SHEET 1 A 3 TRP A 30 GLU A 32 0
SHEET 2 A 3 TRP A 57 CYS A 59 -1 O ARG A 58 N LEU A 31
SHEET 3 A 3 MET A 65 VAL A 66 -1 O VAL A 66 N TRP A 57
LINK ND1 HIS A 28 ZN ZN A 201 1555 1555 2.33
LINK SG CYS A 41 ZN ZN A 401 1555 1555 2.33
LINK SG CYS A 44 ZN ZN A 401 1555 1555 2.33
LINK SG CYS A 59 ZN ZN A 201 1555 1555 2.33
LINK SG CYS A 62 ZN ZN A 201 1555 1555 2.33
LINK ND1 HIS A 67 ZN ZN A 401 1555 1555 2.33
LINK SG CYS A 70 ZN ZN A 401 1555 1555 2.33
LINK SG CYS A 78 ZN ZN A 201 1555 1555 2.33
SITE 1 AC1 4 HIS A 28 CYS A 59 CYS A 62 CYS A 78
SITE 1 AC2 4 CYS A 41 CYS A 44 HIS A 67 CYS A 70
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END