HEADER HYDROLASE 02-JUL-09 2KLH TITLE NMR STRUCTURE OF RCL IN COMPLEX WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-MYC-RESPONSIVE PROTEIN RCL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES IN UNP 11-151; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: RCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BLI5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET24A KEYWDS PROTEIN, GMP, N-GLYCOSIDASE, NUCLEUS, PHOSPHOPROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.PADILLA,Y.YANG,G.LABESSE,C.ZHANG,P.A.KAMINSKI REVDAT 3 10-NOV-21 2KLH 1 REMARK SEQADV REVDAT 2 02-JAN-13 2KLH 1 JRNL VERSN REVDAT 1 20-OCT-09 2KLH 0 JRNL AUTH Y.YANG,A.PADILLA,C.ZHANG,G.LABESSE,P.A.KAMINSKI JRNL TITL STRUCTURAL CHARACTERIZATION OF THE MAMMALIAN DEOXYNUCLEOTIDE JRNL TITL 2 N-HYDROLASE RCL AND ITS STABILIZING INTERACTIONS WITH TWO JRNL TITL 3 INHIBITORS JRNL REF J.MOL.BIOL. V. 394 435 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19822152 JRNL DOI 10.1016/J.JMB.2009.10.004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NCS NON-CRYSTALLOGRAPHIC CONSTRAINTS REMARK 4 REMARK 4 2KLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 300; 300 REMARK 210 PH : 7.2; 7.2; 7.2 REMARK 210 IONIC STRENGTH : 0.05; 0.05; 0.05 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM; REMARK 210 AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.4-0.7 MM [U-100% 15N] RCL-1, REMARK 210 2.0-5.0 MM GUANOSINE-5'- REMARK 210 MONOPHOSPHATE-2, 90% H2O/10% D2O; REMARK 210 0.4-0.7 MM [U-100% 13C; U-100% REMARK 210 15N] RCL-3, 2.0-5.0 MM GUANOSINE- REMARK 210 5'-MONOPHOSPHATE-4, 90% H2O/10% REMARK 210 D2O; 0.4-0.7 MM [U-100% 13C] RCL- REMARK 210 5, 2.0-5.0 MM GUANOSINE-5'- REMARK 210 MONOPHOSPHATE-6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 3D HNCO; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HCACO; 2D 1H-13C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LEU A 42 -124.55 -100.47 REMARK 500 1 THR A 43 52.57 24.81 REMARK 500 1 VAL A 46 39.69 -84.75 REMARK 500 1 ALA A 47 49.83 -178.07 REMARK 500 1 ALA A 49 59.24 -101.00 REMARK 500 1 GLU A 50 66.90 174.72 REMARK 500 1 LEU A 51 105.49 -52.68 REMARK 500 1 GLU A 52 109.29 -55.42 REMARK 500 1 PRO A 53 -165.38 -71.94 REMARK 500 1 LEU A 54 166.25 67.59 REMARK 500 1 ALA A 76 106.94 -59.17 REMARK 500 1 LYS A 102 -62.48 -167.70 REMARK 500 1 SER A 127 -75.25 -67.48 REMARK 500 1 GLU A 136 -102.66 50.92 REMARK 500 1 HIS A 155 173.15 177.80 REMARK 500 1 LEU B 42 -124.59 -100.50 REMARK 500 1 THR B 43 52.61 24.80 REMARK 500 1 VAL B 46 39.69 -84.82 REMARK 500 1 ALA B 47 49.91 -178.04 REMARK 500 1 ALA B 49 59.31 -100.97 REMARK 500 1 GLU B 50 66.91 174.68 REMARK 500 1 LEU B 51 105.54 -52.73 REMARK 500 1 GLU B 52 109.35 -55.46 REMARK 500 1 PRO B 53 -165.34 -72.00 REMARK 500 1 LEU B 54 166.26 67.59 REMARK 500 1 ALA B 76 106.93 -59.11 REMARK 500 1 LYS B 102 -62.42 -167.74 REMARK 500 1 SER B 127 -75.27 -67.42 REMARK 500 1 GLU B 136 -102.65 50.89 REMARK 500 1 HIS B 155 173.11 177.79 REMARK 500 2 SER A 17 102.10 50.59 REMARK 500 2 GLU A 50 68.56 170.18 REMARK 500 2 LEU A 51 100.85 -47.27 REMARK 500 2 GLU A 52 105.78 -49.45 REMARK 500 2 ALA A 58 55.58 -164.64 REMARK 500 2 ALA A 76 105.25 -56.15 REMARK 500 2 PRO A 86 99.03 -60.76 REMARK 500 2 LYS A 102 -60.71 -167.24 REMARK 500 2 GLN A 111 22.59 -150.67 REMARK 500 2 LEU A 116 -101.36 -75.95 REMARK 500 2 SER A 117 168.28 170.55 REMARK 500 2 SER A 127 -73.62 -69.43 REMARK 500 2 GLU A 136 -102.65 50.90 REMARK 500 2 HIS A 155 -71.26 -165.96 REMARK 500 2 HIS A 156 130.83 -174.26 REMARK 500 2 SER B 17 102.08 50.71 REMARK 500 2 GLU B 50 68.59 170.24 REMARK 500 2 LEU B 51 100.84 -47.27 REMARK 500 2 GLU B 52 105.79 -49.50 REMARK 500 2 ALA B 58 55.66 -164.59 REMARK 500 REMARK 500 THIS ENTRY HAS 265 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 187 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP B 187 DBREF 2KLH A 11 151 UNP O35820 RCL_RAT 11 151 DBREF 2KLH B 11 151 UNP O35820 RCL_RAT 11 151 SEQADV 2KLH MET A 8 UNP O35820 EXPRESSION TAG SEQADV 2KLH ARG A 9 UNP O35820 EXPRESSION TAG SEQADV 2KLH ARG A 10 UNP O35820 EXPRESSION TAG SEQADV 2KLH ALA A 69 UNP O35820 ASP 69 ENGINEERED MUTATION SEQADV 2KLH VAL A 152 UNP O35820 EXPRESSION TAG SEQADV 2KLH GLU A 153 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 154 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 155 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 156 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 157 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 158 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS A 159 UNP O35820 EXPRESSION TAG SEQADV 2KLH MET B 8 UNP O35820 EXPRESSION TAG SEQADV 2KLH ARG B 9 UNP O35820 EXPRESSION TAG SEQADV 2KLH ARG B 10 UNP O35820 EXPRESSION TAG SEQADV 2KLH ALA B 69 UNP O35820 ASP 69 ENGINEERED MUTATION SEQADV 2KLH VAL B 152 UNP O35820 EXPRESSION TAG SEQADV 2KLH GLU B 153 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 154 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 155 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 156 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 157 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 158 UNP O35820 EXPRESSION TAG SEQADV 2KLH HIS B 159 UNP O35820 EXPRESSION TAG SEQRES 1 A 152 MET ARG ARG SER VAL TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 A 152 GLY ARG GLU ASP GLN ALA LEU TYR ALA ARG ILE VAL SER SEQRES 3 A 152 ARG LEU ARG ARG TYR GLY LYS VAL LEU THR GLU HIS VAL SEQRES 4 A 152 ALA ASP ALA GLU LEU GLU PRO LEU GLY GLU GLU ALA ALA SEQRES 5 A 152 GLY GLY ASP GLN PHE ILE HIS GLU GLN ALA LEU ASN TRP SEQRES 6 A 152 LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR GLN SEQRES 7 A 152 PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA VAL SEQRES 8 A 152 ALA LEU GLY LYS PRO ILE LEU CYS LEU PHE ARG PRO GLN SEQRES 9 A 152 SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA ALA SEQRES 10 A 152 ASP GLY SER ARG PHE GLN VAL TRP ASP TYR ALA GLU GLY SEQRES 11 A 152 GLU VAL GLU THR MET LEU ASP ARG TYR PHE GLU ALA TYR SEQRES 12 A 152 LEU VAL GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 152 MET ARG ARG SER VAL TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 B 152 GLY ARG GLU ASP GLN ALA LEU TYR ALA ARG ILE VAL SER SEQRES 3 B 152 ARG LEU ARG ARG TYR GLY LYS VAL LEU THR GLU HIS VAL SEQRES 4 B 152 ALA ASP ALA GLU LEU GLU PRO LEU GLY GLU GLU ALA ALA SEQRES 5 B 152 GLY GLY ASP GLN PHE ILE HIS GLU GLN ALA LEU ASN TRP SEQRES 6 B 152 LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR GLN SEQRES 7 B 152 PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA VAL SEQRES 8 B 152 ALA LEU GLY LYS PRO ILE LEU CYS LEU PHE ARG PRO GLN SEQRES 9 B 152 SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA ALA SEQRES 10 B 152 ASP GLY SER ARG PHE GLN VAL TRP ASP TYR ALA GLU GLY SEQRES 11 B 152 GLU VAL GLU THR MET LEU ASP ARG TYR PHE GLU ALA TYR SEQRES 12 B 152 LEU VAL GLU HIS HIS HIS HIS HIS HIS HET 5GP A 187 37 HET 5GP B 187 37 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 5GP 2(C10 H14 N5 O8 P) HELIX 1 1 ASP A 24 GLY A 39 1 16 HELIX 2 2 GLU A 44 ASP A 48 5 5 HELIX 3 3 GLY A 61 ALA A 76 1 16 HELIX 4 4 SER A 87 GLY A 101 1 15 HELIX 5 5 SER A 117 ALA A 124 1 8 HELIX 6 6 ALA A 135 GLY A 137 5 3 HELIX 7 7 GLU A 138 HIS A 154 1 17 HELIX 8 8 ASP B 24 GLY B 39 1 16 HELIX 9 9 GLU B 44 ASP B 48 5 5 HELIX 10 10 GLY B 61 ALA B 76 1 16 HELIX 11 11 SER B 87 GLY B 101 1 15 HELIX 12 12 SER B 117 ALA B 124 1 8 HELIX 13 13 ALA B 135 GLY B 137 5 3 HELIX 14 14 GLU B 138 HIS B 154 1 17 SHEET 1 A 5 LYS A 40 VAL A 41 0 SHEET 2 A 5 SER A 11 CYS A 15 1 N VAL A 12 O LYS A 40 SHEET 3 A 5 VAL A 78 GLU A 82 1 O VAL A 80 N TYR A 13 SHEET 4 A 5 ILE A 104 PHE A 108 1 O LEU A 105 N VAL A 79 SHEET 5 A 5 PHE A 129 ASP A 133 1 O GLN A 130 N CYS A 106 SHEET 1 B 5 LYS B 40 VAL B 41 0 SHEET 2 B 5 SER B 11 CYS B 15 1 N VAL B 12 O LYS B 40 SHEET 3 B 5 VAL B 78 GLU B 82 1 O VAL B 80 N TYR B 13 SHEET 4 B 5 ILE B 104 PHE B 108 1 O LEU B 105 N VAL B 79 SHEET 5 B 5 PHE B 129 ASP B 133 1 O GLN B 130 N CYS B 106 SITE 1 AC1 18 TYR A 13 CYS A 15 GLY A 16 SER A 17 SITE 2 AC1 18 ILE A 18 ARG A 19 TYR A 28 THR A 43 SITE 3 AC1 18 HIS A 45 ILE A 65 GLN A 68 ALA A 69 SITE 4 AC1 18 TRP A 72 GLY A 89 GLU A 93 SER B 117 SITE 5 AC1 18 ALA B 118 MET B 119 SITE 1 AC2 18 SER A 117 ALA A 118 MET A 119 TYR B 13 SITE 2 AC2 18 CYS B 15 GLY B 16 SER B 17 ILE B 18 SITE 3 AC2 18 ARG B 19 TYR B 28 THR B 43 HIS B 45 SITE 4 AC2 18 ILE B 65 GLN B 68 ALA B 69 TRP B 72 SITE 5 AC2 18 GLY B 89 GLU B 93 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