PDB Short entry for 2RSV HEADER TRANSFERASE 12-JUL-12 2RSV TITLE SOLUTION STRUCTURE OF HUMAN FULL-LENGTH VACCINIA RELATED KINASE 1 TITLE 2 (VRK1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE VRK1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VACCINIA-RELATED KINASE 1; COMPND 5 EC: 2.7.11.1; COMPND 6 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: VRK1; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: P060908-04 KEYWDS VRK, KINASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR S.KOSHIBA,N.TOCHIO,J.YOKOYAMA,T.KIGAWA REVDAT 2 14-JUN-23 2RSV 1 REMARK SEQADV REVDAT 1 04-DEC-13 2RSV 0 JRNL AUTH S.KOSHIBA,N.TOCHIO,J.YOKOYAMA,H.YOON,T.KIGAWA JRNL TITL A STRATEGY FOR STRUCTURE DETERMINATION OF LARGE MOLECULAR JRNL TITL 2 WEIGHT PROTEIN USING ISOTOPE LABELING METHODOLOGY WITH JRNL TITL 3 CELL-FREE PROTEIN SYSTHESIS: APPLICATION TO 45 KDA HUMAN JRNL TITL 4 VACCINIA RELATED KIANSE 1 (VRK1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000150242. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-13C; U-15N; U-2H; 1H REMARK 210 ILE, LEU, VAL, ALA METHYL; 1H REMARK 210 MET METHYL,GAMMA; 1H PHE EPSILON] REMARK 210 VRK1, 20 MM [U-2H] TRIS,100 MM REMARK 210 SODIUM CHLORIDE, 50 MM GLUTAMIC REMARK 210 ACID, 50 MM ARGININE, 1 MM [U-2H] REMARK 210 DTT, 0.02 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-13C; U- REMARK 210 15N; U-2H; 1H ILE, LEU, VAL REMARK 210 METHYL; 1H PHE, TYR EPSILON] REMARK 210 VRK1, 20 MM [U-2H] TRIS,100 MM REMARK 210 SODIUM CHLORIDE, 50 MM GLUTAMIC REMARK 210 ACID, 50 MM ARGININE, 1 MM [U-2H] REMARK 210 DTT, 0.02 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-15N; U-2H; REMARK 210 13C,1H ILE, LEU, VAL METHYL; REMARK 210 13C,1H PHE DELTA/EPSILON/ZETA] REMARK 210 VRK1, 20 MM [U-2H] TRIS,100 MM REMARK 210 SODIUM CHLORIDE, 50 MM GLUTAMIC REMARK 210 ACID, 50 MM ARGININE, 1 MM [U-2H] REMARK 210 DTT, 0.02 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O; 0.4 MM SAIL-VRK1, REMARK 210 20 MM [U-2H] TRIS, 100 MM SODIUM REMARK 210 CHLORIDE, 50 MM GLUTAMIC ACID, REMARK 210 50 MM ARGININE, 1 MM [U-2H] DTT, REMARK 210 0.02 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D 13C-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, AZARA, NMRVIEW, KUJIRA, REMARK 210 CNS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 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: 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: 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 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 SER A -2 -177.33 60.51 REMARK 500 1 VAL A 4 -67.25 69.10 REMARK 500 1 ARG A 11 88.23 -173.37 REMARK 500 1 GLN A 12 -64.62 -144.64 REMARK 500 1 SER A 13 -68.68 68.25 REMARK 500 1 SER A 14 172.65 59.99 REMARK 500 1 ALA A 15 -50.18 -164.82 REMARK 500 1 ARG A 17 -45.16 -135.91 REMARK 500 1 HIS A 18 103.79 -169.32 REMARK 500 1 LEU A 19 -179.47 -69.64 REMARK 500 1 GLN A 22 -78.63 -88.40 REMARK 500 1 ASP A 31 -144.63 -83.03 REMARK 500 1 ILE A 43 30.89 -141.61 REMARK 500 1 PHE A 48 -69.13 -121.20 REMARK 500 1 SER A 61 125.63 63.42 REMARK 500 1 PRO A 67 42.50 -84.04 REMARK 500 1 PRO A 74 82.02 -69.37 REMARK 500 1 SER A 75 122.89 62.28 REMARK 500 1 ASN A 77 75.00 -154.88 REMARK 500 1 TYR A 107 -73.18 -176.86 REMARK 500 1 LEU A 108 158.23 59.96 REMARK 500 1 ARG A 133 -78.24 -148.09 REMARK 500 1 PHE A 134 125.22 64.19 REMARK 500 1 ALA A 146 44.24 92.56 REMARK 500 1 ARG A 148 121.46 -170.72 REMARK 500 1 GLU A 172 40.25 74.75 REMARK 500 1 ASP A 177 82.31 72.73 REMARK 500 1 ASP A 191 -36.33 -177.50 REMARK 500 1 ASP A 197 111.63 62.47 REMARK 500 1 TYR A 198 -57.39 -145.47 REMARK 500 1 LEU A 200 33.87 -96.56 REMARK 500 1 ALA A 201 -90.24 -131.08 REMARK 500 1 ARG A 203 47.21 -94.82 REMARK 500 1 TYR A 204 94.64 58.44 REMARK 500 1 CYS A 205 163.91 58.52 REMARK 500 1 PRO A 206 -167.66 -68.96 REMARK 500 1 LYS A 214 -56.42 -145.28 REMARK 500 1 PRO A 217 71.37 -67.46 REMARK 500 1 LYS A 218 -46.13 -149.68 REMARK 500 1 CYS A 220 -68.27 -102.11 REMARK 500 1 THR A 224 -52.94 -127.75 REMARK 500 1 ILE A 225 38.85 -179.09 REMARK 500 1 ALA A 237 151.88 61.56 REMARK 500 1 ARG A 240 -50.82 -144.87 REMARK 500 1 HIS A 258 144.89 62.41 REMARK 500 1 PRO A 260 64.41 -67.99 REMARK 500 1 TRP A 261 -40.67 -178.90 REMARK 500 1 PRO A 296 -162.99 -56.86 REMARK 500 1 LEU A 309 87.61 -57.95 REMARK 500 1 ASP A 310 -43.91 -170.84 REMARK 500 REMARK 500 THIS ENTRY HAS 1238 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11506 RELATED DB: BMRB DBREF 2RSV A 1 396 UNP Q99986 VRK1_HUMAN 1 396 SEQADV 2RSV GLY A -6 UNP Q99986 EXPRESSION TAG SEQADV 2RSV SER A -5 UNP Q99986 EXPRESSION TAG SEQADV 2RSV SER A -4 UNP Q99986 EXPRESSION TAG SEQADV 2RSV GLY A -3 UNP Q99986 EXPRESSION TAG SEQADV 2RSV SER A -2 UNP Q99986 EXPRESSION TAG SEQADV 2RSV SER A -1 UNP Q99986 EXPRESSION TAG SEQADV 2RSV GLY A 0 UNP Q99986 EXPRESSION TAG SEQRES 1 A 403 GLY SER SER GLY SER SER GLY MET PRO ARG VAL LYS ALA SEQRES 2 A 403 ALA GLN ALA GLY ARG GLN SER SER ALA LYS ARG HIS LEU SEQRES 3 A 403 ALA GLU GLN PHE ALA VAL GLY GLU ILE ILE THR ASP MET SEQRES 4 A 403 ALA LYS LYS GLU TRP LYS VAL GLY LEU PRO ILE GLY GLN SEQRES 5 A 403 GLY GLY PHE GLY CYS ILE TYR LEU ALA ASP MET ASN SER SEQRES 6 A 403 SER GLU SER VAL GLY SER ASP ALA PRO CYS VAL VAL LYS SEQRES 7 A 403 VAL GLU PRO SER ASP ASN GLY PRO LEU PHE THR GLU LEU SEQRES 8 A 403 LYS PHE TYR GLN ARG ALA ALA LYS PRO GLU GLN ILE GLN SEQRES 9 A 403 LYS TRP ILE ARG THR ARG LYS LEU LYS TYR LEU GLY VAL SEQRES 10 A 403 PRO LYS TYR TRP GLY SER GLY LEU HIS ASP LYS ASN GLY SEQRES 11 A 403 LYS SER TYR ARG PHE MET ILE MET ASP ARG PHE GLY SER SEQRES 12 A 403 ASP LEU GLN LYS ILE TYR GLU ALA ASN ALA LYS ARG PHE SEQRES 13 A 403 SER ARG LYS THR VAL LEU GLN LEU SER LEU ARG ILE LEU SEQRES 14 A 403 ASP ILE LEU GLU TYR ILE HIS GLU HIS GLU TYR VAL HIS SEQRES 15 A 403 GLY ASP ILE LYS ALA SER ASN LEU LEU LEU ASN TYR LYS SEQRES 16 A 403 ASN PRO ASP GLN VAL TYR LEU VAL ASP TYR GLY LEU ALA SEQRES 17 A 403 TYR ARG TYR CYS PRO GLU GLY VAL HIS LYS GLU TYR LYS SEQRES 18 A 403 GLU ASP PRO LYS ARG CYS HIS ASP GLY THR ILE GLU PHE SEQRES 19 A 403 THR SER ILE ASP ALA HIS ASN GLY VAL ALA PRO SER ARG SEQRES 20 A 403 ARG GLY ASP LEU GLU ILE LEU GLY TYR CYS MET ILE GLN SEQRES 21 A 403 TRP LEU THR GLY HIS LEU PRO TRP GLU ASP ASN LEU LYS SEQRES 22 A 403 ASP PRO LYS TYR VAL ARG ASP SER LYS ILE ARG TYR ARG SEQRES 23 A 403 GLU ASN ILE ALA SER LEU MET ASP LYS CYS PHE PRO GLU SEQRES 24 A 403 LYS ASN LYS PRO GLY GLU ILE ALA LYS TYR MET GLU THR SEQRES 25 A 403 VAL LYS LEU LEU ASP TYR THR GLU LYS PRO LEU TYR GLU SEQRES 26 A 403 ASN LEU ARG ASP ILE LEU LEU GLN GLY LEU LYS ALA ILE SEQRES 27 A 403 GLY SER LYS ASP ASP GLY LYS LEU ASP LEU SER VAL VAL SEQRES 28 A 403 GLU ASN GLY GLY LEU LYS ALA LYS THR ILE THR LYS LYS SEQRES 29 A 403 ARG LYS LYS GLU ILE GLU GLU SER LYS GLU PRO GLY VAL SEQRES 30 A 403 GLU ASP THR GLU TRP SER ASN THR GLN THR GLU GLU ALA SEQRES 31 A 403 ILE GLN THR ARG SER ARG THR ARG LYS ARG VAL GLN LYS HELIX 1 1 GLY A 78 ALA A 90 1 13 HELIX 2 2 LYS A 92 LYS A 104 1 13 HELIX 3 3 ASP A 137 ASN A 145 1 9 HELIX 4 4 SER A 150 HIS A 171 1 22 HELIX 5 5 SER A 229 ASN A 234 1 6 HELIX 6 6 ARG A 241 GLY A 257 1 17 HELIX 7 7 ASP A 267 ARG A 279 1 13 HELIX 8 8 ASN A 281 PHE A 290 1 10 HELIX 9 9 GLY A 297 LEU A 309 1 13 HELIX 10 10 LEU A 316 GLY A 327 1 12 HELIX 11 11 LEU A 328 ALA A 330 5 3 SHEET 1 A 6 ILE A 28 THR A 30 0 SHEET 2 A 6 GLU A 36 VAL A 39 -1 O TRP A 37 N ILE A 29 SHEET 3 A 6 ILE A 51 ASP A 55 -1 O ASP A 55 N LYS A 38 SHEET 4 A 6 VAL A 69 GLU A 73 -1 O VAL A 70 N TYR A 52 SHEET 5 A 6 LYS A 124 MET A 131 -1 O MET A 131 N VAL A 69 SHEET 6 A 6 TYR A 113 LYS A 121 -1 N LYS A 121 O LYS A 124 SHEET 1 B 2 LEU A 183 LEU A 185 0 SHEET 2 B 2 VAL A 193 LEU A 195 -1 O TYR A 194 N LEU A 184 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