PDB Short entry for 2KDC HEADER TRANSFERASE 06-JAN-09 2KDC TITLE NMR SOLUTION STRUCTURE OF E. COLI DIACYLGLYCEROL KINASE (DAGK) IN DPC TITLE 2 MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIACYLGLYCEROL KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DAGK, DIGLYCERIDE KINASE, DGK; COMPND 5 EC: 2.7.1.107; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DGKA, B4042, JW4002; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PSD004 KEYWDS MEMBRANE PROTEIN, KINASE, DAGK, CELL INNER MEMBRANE, CELL MEMBRANE, KEYWDS 2 MEMBRANE, PHOSPHOLIPID BIOSYNTHESIS, TRANSFERASE, TRANSMEMBRANE EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR W.D.VAN HORN,H.KIM,C.D.ELLIS,A.HADZISELIMOVIC,E.S.SULISTIJO, AUTHOR 2 M.D.KARRA,C.TIAN,F.D.SONNICHSEN,C.R.SANDERS REVDAT 2 16-MAR-22 2KDC 1 REMARK REVDAT 1 07-JUL-09 2KDC 0 JRNL AUTH W.D.VAN HORN,H.J.KIM,C.D.ELLIS,A.HADZISELIMOVIC, JRNL AUTH 2 E.S.SULISTIJO,M.D.KARRA,C.TIAN,F.D.SONNICHSEN,C.R.SANDERS JRNL TITL SOLUTION NUCLEAR MAGNETIC RESONANCE STRUCTURE OF JRNL TITL 2 MEMBRANE-INTEGRAL DIACYLGLYCEROL KINASE JRNL REF SCIENCE V. 324 1726 2009 JRNL REFN ISSN 0036-8075 JRNL PMID 19556511 JRNL DOI 10.1126/SCIENCE.1171716 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.19, X-PLOR NIH 2.19 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED REFINE.PY FROM XPLOR-NIH REMARK 4 REMARK 4 2KDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100979. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-100% 15N] DAGK, 90% REMARK 210 H2O/10% D2O; 1.4 MM [ U-15N; U- REMARK 210 2H] DAGK, 90% H2O/10% D2O; 1.0 REMARK 210 MM [U-100% 15N] DAGK, 90% H2O/10% REMARK 210 D2O; 1.0 MM [U-13C; U-15N; U-2H] REMARK 210 DAGK, 90% H2O/10% D2O; 1.0 MM REMARK 210 [U-100% 13C; U-100% 15N; U-80% REMARK 210 2H] DAGK, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TROSY 1H-15N HSQC; 3D TROSY REMARK 210 HNCO; 3D TROSY HNCA; 3D TROSY REMARK 210 HN(CO)CA; 3D TROSY CBCA(CO)NH; REMARK 210 3D TROSY HNCACB; 3D 1H-15N TROSY REMARK 210 - NOESY; 2D TROSY 1H-15N HQSC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5, TALOS, SPARKY, REMARK 210 NMRDRAW, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 48 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O VAL B 56 H SER B 60 1.51 REMARK 500 O VAL C 56 H SER C 60 1.52 REMARK 500 O VAL A 56 H SER A 60 1.52 REMARK 500 O ILE C 70 H SER C 73 1.58 REMARK 500 O ILE B 70 H SER B 73 1.58 REMARK 500 O ILE A 70 H SER A 73 1.58 REMARK 500 O ALA A 37 H ALA A 41 1.59 REMARK 500 O ALA B 37 H ALA B 41 1.59 REMARK 500 O VAL B 107 H THR B 111 1.59 REMARK 500 O VAL A 107 H THR A 111 1.59 REMARK 500 O ALA C 37 H ALA C 41 1.59 REMARK 500 O VAL C 107 H THR C 111 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 4 77.25 50.93 REMARK 500 1 ASN A 27 43.31 -107.79 REMARK 500 1 GLU A 28 -70.61 164.59 REMARK 500 1 VAL A 38 -19.25 -38.44 REMARK 500 1 LEU A 48 132.46 -173.36 REMARK 500 1 VAL A 50 51.78 -154.91 REMARK 500 1 ILE A 53 -2.31 69.51 REMARK 500 1 ASP A 80 -103.55 -78.17 REMARK 500 1 ILE A 82 98.55 34.23 REMARK 500 1 SER A 84 170.78 -54.73 REMARK 500 1 LEU A 89 -44.00 177.64 REMARK 500 1 SER A 90 39.74 -70.52 REMARK 500 1 VAL A 107 -70.24 -48.71 REMARK 500 1 ALA A 108 -32.59 -32.54 REMARK 500 1 VAL A 109 -75.52 -89.27 REMARK 500 1 THR B 4 77.34 50.93 REMARK 500 1 ASN B 27 43.33 -107.83 REMARK 500 1 GLU B 28 -70.69 164.52 REMARK 500 1 VAL B 38 -19.30 -38.35 REMARK 500 1 LEU B 48 132.32 -173.25 REMARK 500 1 VAL B 50 51.89 -154.96 REMARK 500 1 ILE B 53 -2.22 69.46 REMARK 500 1 ASP B 80 -103.58 -78.21 REMARK 500 1 ILE B 82 98.53 34.31 REMARK 500 1 SER B 84 170.71 -54.58 REMARK 500 1 LEU B 89 -44.02 177.60 REMARK 500 1 SER B 90 39.67 -70.53 REMARK 500 1 VAL B 107 -70.20 -48.71 REMARK 500 1 ALA B 108 -32.79 -32.44 REMARK 500 1 VAL B 109 -75.49 -89.24 REMARK 500 1 THR C 4 77.29 50.93 REMARK 500 1 ASN C 27 43.27 -107.75 REMARK 500 1 GLU C 28 -70.70 164.56 REMARK 500 1 VAL C 38 -19.22 -38.51 REMARK 500 1 LEU C 48 132.41 -173.30 REMARK 500 1 VAL C 50 51.87 -154.94 REMARK 500 1 ILE C 53 -2.21 69.49 REMARK 500 1 ASP C 80 -103.57 -78.10 REMARK 500 1 ILE C 82 98.40 34.43 REMARK 500 1 SER C 84 170.76 -54.72 REMARK 500 1 LEU C 89 -43.97 177.58 REMARK 500 1 SER C 90 39.64 -70.49 REMARK 500 1 VAL C 107 -70.09 -48.90 REMARK 500 1 ALA C 108 -32.78 -32.42 REMARK 500 1 VAL C 109 -75.36 -89.26 REMARK 500 2 THR A 4 -59.82 -161.28 REMARK 500 2 THR A 5 -43.64 -161.73 REMARK 500 2 ALA A 29 -2.85 -57.79 REMARK 500 2 ALA A 30 -22.38 -39.15 REMARK 500 2 LEU A 48 103.15 -169.14 REMARK 500 REMARK 500 THIS ENTRY HAS 931 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15019 RELATED DB: BMRB REMARK 900 NMR ASSIGNMENTS FOR A HELICAL DIACYLGLYCEROL KINASE (DAGK), 40 KDA REMARK 900 MEMBRANE PROTEIN FROM E. COLI DBREF 2KDC A 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 DBREF 2KDC B 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 DBREF 2KDC C 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 SEQRES 1 A 121 ALA ASN ASN THR THR GLY PHE THR ARG ILE ILE LYS ALA SEQRES 2 A 121 ALA GLY TYR SER TRP LYS GLY LEU ARG ALA ALA TRP ILE SEQRES 3 A 121 ASN GLU ALA ALA PHE ARG GLN GLU GLY VAL ALA VAL LEU SEQRES 4 A 121 LEU ALA VAL VAL ILE ALA CYS TRP LEU ASP VAL ASP ALA SEQRES 5 A 121 ILE THR ARG VAL LEU LEU ILE SER SER VAL MET LEU VAL SEQRES 6 A 121 MET ILE VAL GLU ILE LEU ASN SER ALA ILE GLU ALA VAL SEQRES 7 A 121 VAL ASP ARG ILE GLY SER GLU TYR HIS GLU LEU SER GLY SEQRES 8 A 121 ARG ALA LYS ASP MET GLY SER ALA ALA VAL LEU ILE ALA SEQRES 9 A 121 ILE ILE VAL ALA VAL ILE THR TRP CYS ILE LEU LEU TRP SEQRES 10 A 121 SER HIS PHE GLY SEQRES 1 B 121 ALA ASN ASN THR THR GLY PHE THR ARG ILE ILE LYS ALA SEQRES 2 B 121 ALA GLY TYR SER TRP LYS GLY LEU ARG ALA ALA TRP ILE SEQRES 3 B 121 ASN GLU ALA ALA PHE ARG GLN GLU GLY VAL ALA VAL LEU SEQRES 4 B 121 LEU ALA VAL VAL ILE ALA CYS TRP LEU ASP VAL ASP ALA SEQRES 5 B 121 ILE THR ARG VAL LEU LEU ILE SER SER VAL MET LEU VAL SEQRES 6 B 121 MET ILE VAL GLU ILE LEU ASN SER ALA ILE GLU ALA VAL SEQRES 7 B 121 VAL ASP ARG ILE GLY SER GLU TYR HIS GLU LEU SER GLY SEQRES 8 B 121 ARG ALA LYS ASP MET GLY SER ALA ALA VAL LEU ILE ALA SEQRES 9 B 121 ILE ILE VAL ALA VAL ILE THR TRP CYS ILE LEU LEU TRP SEQRES 10 B 121 SER HIS PHE GLY SEQRES 1 C 121 ALA ASN ASN THR THR GLY PHE THR ARG ILE ILE LYS ALA SEQRES 2 C 121 ALA GLY TYR SER TRP LYS GLY LEU ARG ALA ALA TRP ILE SEQRES 3 C 121 ASN GLU ALA ALA PHE ARG GLN GLU GLY VAL ALA VAL LEU SEQRES 4 C 121 LEU ALA VAL VAL ILE ALA CYS TRP LEU ASP VAL ASP ALA SEQRES 5 C 121 ILE THR ARG VAL LEU LEU ILE SER SER VAL MET LEU VAL SEQRES 6 C 121 MET ILE VAL GLU ILE LEU ASN SER ALA ILE GLU ALA VAL SEQRES 7 C 121 VAL ASP ARG ILE GLY SER GLU TYR HIS GLU LEU SER GLY SEQRES 8 C 121 ARG ALA LYS ASP MET GLY SER ALA ALA VAL LEU ILE ALA SEQRES 9 C 121 ILE ILE VAL ALA VAL ILE THR TRP CYS ILE LEU LEU TRP SEQRES 10 C 121 SER HIS PHE GLY HELIX 1 1 GLY A 6 TYR A 16 1 11 HELIX 2 2 TYR A 16 TRP A 25 1 10 HELIX 3 3 ALA A 29 LEU A 48 1 20 HELIX 4 4 ILE A 53 ILE A 70 1 18 HELIX 5 5 ILE A 70 ASP A 80 1 11 HELIX 6 6 SER A 90 SER A 118 1 29 HELIX 7 7 GLY B 6 TYR B 16 1 11 HELIX 8 8 TYR B 16 TRP B 25 1 10 HELIX 9 9 ALA B 29 LEU B 48 1 20 HELIX 10 10 ILE B 53 ILE B 70 1 18 HELIX 11 11 ILE B 70 ASP B 80 1 11 HELIX 12 12 SER B 90 SER B 118 1 29 HELIX 13 13 GLY C 6 TYR C 16 1 11 HELIX 14 14 TYR C 16 TRP C 25 1 10 HELIX 15 15 ALA C 29 LEU C 48 1 20 HELIX 16 16 ILE C 53 ILE C 70 1 18 HELIX 17 17 ILE C 70 ASP C 80 1 11 HELIX 18 18 SER C 90 SER C 118 1 29 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