HEADER RNA BINDING PROTEIN 11-DEC-14 4X9D TITLE HIGH-RESOLUTION STRUCTURE OF HFQ FROM METHANOCOCCUS JANNASCHII IN TITLE 2 COMPLEX WITH UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN MJ1435; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ1435; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PUBS520 KEYWDS HFQ, ARCHAEAL LSM, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.D.NIKULIN,S.V.TISHCHENKO,E.Y.NIKONOVA,V.N.MURINA,A.O.MIHAILINA, AUTHOR 2 N.V.LEKONTSEVA REVDAT 4 10-JAN-24 4X9D 1 LINK REVDAT 3 24-MAY-17 4X9D 1 JRNL REVDAT 2 22-FEB-17 4X9D 1 JRNL REVDAT 1 23-DEC-15 4X9D 0 JRNL AUTH A.NIKULIN,A.MIKHAILINA,N.LEKONTSEVA,V.BALOBANOV,E.NIKONOVA, JRNL AUTH 2 S.TISHCHENKO JRNL TITL CHARACTERIZATION OF RNA-BINDING PROPERTIES OF THE ARCHAEAL JRNL TITL 2 HFQ-LIKE PROTEIN FROM METHANOCOCCUS JANNASCHII. JRNL REF J. BIOMOL. STRUCT. DYN. V. 35 1615 2017 JRNL REFN ESSN 1538-0254 JRNL PMID 27187760 JRNL DOI 10.1080/07391102.2016.1189849 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 68657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 3403 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.7228 - 4.3144 1.00 2947 148 0.1736 0.1922 REMARK 3 2 4.3144 - 3.4249 1.00 2815 133 0.1573 0.1879 REMARK 3 3 3.4249 - 2.9921 1.00 2797 140 0.1668 0.1953 REMARK 3 4 2.9921 - 2.7185 1.00 2765 144 0.1770 0.2026 REMARK 3 5 2.7185 - 2.5237 1.00 2735 145 0.1819 0.2105 REMARK 3 6 2.5237 - 2.3749 1.00 2733 145 0.1704 0.2101 REMARK 3 7 2.3749 - 2.2560 1.00 2768 143 0.1653 0.1991 REMARK 3 8 2.2560 - 2.1578 1.00 2702 139 0.1536 0.1866 REMARK 3 9 2.1578 - 2.0747 1.00 2728 160 0.1638 0.1861 REMARK 3 10 2.0747 - 2.0031 1.00 2698 148 0.1655 0.2009 REMARK 3 11 2.0031 - 1.9405 1.00 2731 137 0.1630 0.1929 REMARK 3 12 1.9405 - 1.8850 1.00 2725 135 0.1596 0.1990 REMARK 3 13 1.8850 - 1.8354 1.00 2717 141 0.1722 0.1811 REMARK 3 14 1.8354 - 1.7906 1.00 2708 145 0.1671 0.1821 REMARK 3 15 1.7906 - 1.7499 1.00 2692 140 0.1771 0.2101 REMARK 3 16 1.7499 - 1.7127 1.00 2717 131 0.1910 0.2483 REMARK 3 17 1.7127 - 1.6784 1.00 2723 145 0.1956 0.2499 REMARK 3 18 1.6784 - 1.6467 1.00 2667 148 0.1956 0.2020 REMARK 3 19 1.6467 - 1.6173 1.00 2718 147 0.2033 0.2564 REMARK 3 20 1.6173 - 1.5899 1.00 2705 134 0.2187 0.2591 REMARK 3 21 1.5899 - 1.5643 1.00 2675 132 0.2199 0.2590 REMARK 3 22 1.5643 - 1.5402 1.00 2707 144 0.2286 0.2476 REMARK 3 23 1.5402 - 1.5175 1.00 2649 152 0.2393 0.2436 REMARK 3 24 1.5175 - 1.4962 0.90 2432 127 0.2711 0.2913 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3126 REMARK 3 ANGLE : 1.111 4209 REMARK 3 CHIRALITY : 0.047 462 REMARK 3 PLANARITY : 0.004 515 REMARK 3 DIHEDRAL : 12.703 1228 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4X9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.86 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07260 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4X9C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A2 JBCSCREEN NUC-PRO 1 (50% PEG200, REMARK 280 0,1M TRIS-HCL, PH 8,0) IN PRESENCE OF 25 MM UMP, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.87050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.43700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.65500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.87050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.43700 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -174.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 GLN A 8 REMARK 465 GLN A 9 REMARK 465 PRO A 10 REMARK 465 LYS A 11 REMARK 465 LYS A 12 REMARK 465 VAL A 13 REMARK 465 ILE A 14 REMARK 465 PRO A 15 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 LYS B 3 REMARK 465 PRO B 4 REMARK 465 VAL B 5 REMARK 465 LYS B 6 REMARK 465 LYS B 7 REMARK 465 GLN B 8 REMARK 465 GLN B 9 REMARK 465 PRO B 10 REMARK 465 LYS B 11 REMARK 465 LYS B 12 REMARK 465 VAL B 13 REMARK 465 MET C 1 REMARK 465 ASN C 2 REMARK 465 LYS C 3 REMARK 465 PRO C 4 REMARK 465 VAL C 5 REMARK 465 LYS C 6 REMARK 465 LYS C 7 REMARK 465 GLN C 8 REMARK 465 GLN C 9 REMARK 465 PRO C 10 REMARK 465 LYS C 11 REMARK 465 LYS C 12 REMARK 465 VAL C 13 REMARK 465 ILE C 14 REMARK 465 PRO C 15 REMARK 465 MET D 1 REMARK 465 ASN D 2 REMARK 465 LYS D 3 REMARK 465 PRO D 4 REMARK 465 VAL D 5 REMARK 465 LYS D 6 REMARK 465 LYS D 7 REMARK 465 GLN D 8 REMARK 465 GLN D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 MET E 1 REMARK 465 ASN E 2 REMARK 465 LYS E 3 REMARK 465 PRO E 4 REMARK 465 VAL E 5 REMARK 465 LYS E 6 REMARK 465 LYS E 7 REMARK 465 GLN E 8 REMARK 465 GLN E 9 REMARK 465 PRO E 10 REMARK 465 LYS E 11 REMARK 465 LYS E 12 REMARK 465 VAL E 13 REMARK 465 ILE E 14 REMARK 465 PRO E 15 REMARK 465 MET F 1 REMARK 465 ASN F 2 REMARK 465 LYS F 3 REMARK 465 PRO F 4 REMARK 465 VAL F 5 REMARK 465 LYS F 6 REMARK 465 LYS F 7 REMARK 465 GLN F 8 REMARK 465 GLN F 9 REMARK 465 PRO F 10 REMARK 465 LYS F 11 REMARK 465 LYS F 12 REMARK 465 VAL F 13 REMARK 465 ILE F 14 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O2P U5P F 104 O HOH F 245 1.89 REMARK 500 N HIS E 64 O3P U5P E 104 2.02 REMARK 500 OE1 GLU D 36 O HOH D 201 2.03 REMARK 500 O1P U5P B 104 O HOH B 239 2.08 REMARK 500 NH2 ARG A 21 OD1 ASN A 47 2.11 REMARK 500 O HOH D 201 O HOH E 202 2.11 REMARK 500 O2 U5P C 104 O HOH C 237 2.12 REMARK 500 O HOH A 226 O HOH B 236 2.13 REMARK 500 O HOH A 228 O HOH B 238 2.15 REMARK 500 O3' U5P B 104 O HOH B 237 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH D 203 O HOH F 210 1455 2.18 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 ASN D 16 46.78 -95.74 REMARK 500 PHE D 17 -69.33 -91.69 REMARK 500 ASN F 16 41.30 -92.99 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 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 48 O REMARK 620 2 U5P B 104 O3' 138.5 REMARK 620 3 U5P B 104 O2' 95.4 51.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U5P A 104 O3' REMARK 620 2 TYR F 48 O 138.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 48 O REMARK 620 2 U5P C 104 O3' 132.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 235 O REMARK 620 2 U5P C 104 O3P 105.4 REMARK 620 3 HOH C 213 O 111.3 141.7 REMARK 620 4 HOH C 240 O 104.4 71.4 108.6 REMARK 620 5 HOH C 241 O 123.1 54.4 95.0 113.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR C 48 O REMARK 620 2 U5P D 101 O3' 133.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P C 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P E 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 F 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA F 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P F 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X9C RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT UMP DBREF 4X9D A 1 71 UNP Q58830 Y1435_METJA 1 71 DBREF 4X9D B 1 71 UNP Q58830 Y1435_METJA 1 71 DBREF 4X9D C 1 71 UNP Q58830 Y1435_METJA 1 71 DBREF 4X9D D 1 71 UNP Q58830 Y1435_METJA 1 71 DBREF 4X9D E 1 71 UNP Q58830 Y1435_METJA 1 71 DBREF 4X9D F 1 71 UNP Q58830 Y1435_METJA 1 71 SEQRES 1 A 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 A 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 A 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 A 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 A 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 A 71 ILE ASP TYR ILE GLU TYR SEQRES 1 B 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 B 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 B 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 B 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 B 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 B 71 ILE ASP TYR ILE GLU TYR SEQRES 1 C 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 C 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 C 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 C 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 C 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 C 71 ILE ASP TYR ILE GLU TYR SEQRES 1 D 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 D 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 D 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 D 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 D 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 D 71 ILE ASP TYR ILE GLU TYR SEQRES 1 E 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 E 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 E 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 E 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 E 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 E 71 ILE ASP TYR ILE GLU TYR SEQRES 1 F 71 MET ASN LYS PRO VAL LYS LYS GLN GLN PRO LYS LYS VAL SEQRES 2 F 71 ILE PRO ASN PHE GLU TYR ALA ARG ARG LEU ASN GLY LYS SEQRES 3 F 71 LYS VAL LYS ILE PHE LEU ARG ASN GLY GLU VAL LEU ASP SEQRES 4 F 71 ALA GLU VAL THR GLY VAL SER ASN TYR GLU ILE MET VAL SEQRES 5 F 71 LYS VAL GLY ASP ARG ASN LEU LEU VAL PHE LYS HIS ALA SEQRES 6 F 71 ILE ASP TYR ILE GLU TYR HET PGE A 101 10 HET SO4 A 102 5 HET NA A 103 1 HET U5P A 104 21 HET EDO B 101 4 HET NA B 102 1 HET NA B 103 1 HET U5P B 104 21 HET PG4 C 101 13 HET NA C 102 1 HET CL C 103 1 HET U5P C 104 21 HET U5P D 101 21 HET PG4 E 101 13 HET PGE E 102 10 HET CL E 103 1 HET U5P E 104 21 HET PEG F 101 7 HET SO4 F 102 5 HET NA F 103 1 HET U5P F 104 21 HETNAM PGE TRIETHYLENE GLYCOL HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EDO ETHYLENE GLYCOL FORMUL 7 PGE 2(C6 H14 O4) FORMUL 8 SO4 2(O4 S 2-) FORMUL 9 NA 5(NA 1+) FORMUL 10 U5P 6(C9 H13 N2 O9 P) FORMUL 11 EDO C2 H6 O2 FORMUL 15 PG4 2(C8 H18 O5) FORMUL 17 CL 2(CL 1-) FORMUL 24 PEG C4 H10 O3 FORMUL 28 HOH *241(H2 O) HELIX 1 AA1 GLU A 18 ASN A 24 5 7 HELIX 2 AA2 TYR B 19 ASN B 24 5 6 HELIX 3 AA3 GLU C 18 ASN C 24 5 7 HELIX 4 AA4 TYR D 19 ASN D 24 5 6 HELIX 5 AA5 TYR E 19 ASN E 24 5 6 HELIX 6 AA6 GLU F 18 ASN F 24 5 7 SHEET 1 AA131 LYS A 27 LEU A 32 0 SHEET 2 AA131 VAL A 37 VAL A 45 -1 O ALA A 40 N VAL A 28 SHEET 3 AA131 GLU A 49 VAL A 54 -1 O MET A 51 N GLY A 44 SHEET 4 AA131 ARG A 57 PHE A 62 -1 O VAL A 61 N ILE A 50 SHEET 5 AA131 ILE B 66 TYR B 71 -1 O ILE B 69 N LEU A 60 SHEET 6 AA131 LYS B 27 LEU B 32 -1 N PHE B 31 O ASP B 67 SHEET 7 AA131 VAL B 37 VAL B 45 -1 O ALA B 40 N VAL B 28 SHEET 8 AA131 GLU B 49 VAL B 54 -1 O MET B 51 N THR B 43 SHEET 9 AA131 ARG B 57 PHE B 62 -1 O VAL B 61 N ILE B 50 SHEET 10 AA131 ILE C 66 TYR C 71 -1 O ILE C 69 N LEU B 60 SHEET 11 AA131 LYS C 27 LEU C 32 -1 N PHE C 31 O ASP C 67 SHEET 12 AA131 VAL C 37 VAL C 45 -1 O ALA C 40 N VAL C 28 SHEET 13 AA131 GLU C 49 VAL C 54 -1 O MET C 51 N THR C 43 SHEET 14 AA131 ARG C 57 PHE C 62 -1 O VAL C 61 N ILE C 50 SHEET 15 AA131 ILE D 66 TYR D 71 -1 O ILE D 69 N LEU C 60 SHEET 16 AA131 LYS D 27 LEU D 32 -1 N PHE D 31 O ASP D 67 SHEET 17 AA131 VAL D 37 VAL D 45 -1 O ALA D 40 N VAL D 28 SHEET 18 AA131 GLU D 49 VAL D 54 -1 O MET D 51 N GLY D 44 SHEET 19 AA131 ARG D 57 PHE D 62 -1 O VAL D 61 N ILE D 50 SHEET 20 AA131 ILE E 66 TYR E 71 -1 O ILE E 69 N LEU D 60 SHEET 21 AA131 LYS E 27 LEU E 32 -1 N PHE E 31 O ASP E 67 SHEET 22 AA131 VAL E 37 VAL E 45 -1 O ALA E 40 N VAL E 28 SHEET 23 AA131 GLU E 49 VAL E 54 -1 O MET E 51 N GLY E 44 SHEET 24 AA131 ARG E 57 PHE E 62 -1 O VAL E 61 N ILE E 50 SHEET 25 AA131 ILE F 66 TYR F 71 -1 O ILE F 69 N LEU E 60 SHEET 26 AA131 LYS F 27 LEU F 32 -1 N PHE F 31 O ASP F 67 SHEET 27 AA131 VAL F 37 VAL F 45 -1 O ALA F 40 N VAL F 28 SHEET 28 AA131 GLU F 49 VAL F 54 -1 O MET F 51 N THR F 43 SHEET 29 AA131 ARG F 57 PHE F 62 -1 O ARG F 57 N VAL F 54 SHEET 30 AA131 ILE A 66 TYR A 71 -1 N ILE A 69 O LEU F 60 SHEET 31 AA131 LYS A 27 LEU A 32 -1 N PHE A 31 O ASP A 67 LINK O TYR A 48 NA NA A 103 1555 1555 2.86 LINK NA NA A 103 O3' U5P B 104 1555 1555 3.15 LINK NA NA A 103 O2' U5P B 104 1555 1555 3.16 LINK O3' U5P A 104 NA NA F 103 1555 1555 2.91 LINK O TYR B 48 NA NA B 103 1555 1555 2.92 LINK NA NA B 102 O HOH B 235 1555 1555 2.81 LINK NA NA B 102 O3P U5P C 104 1555 1555 2.37 LINK NA NA B 102 O HOH C 213 1555 1555 2.72 LINK NA NA B 102 O HOH C 240 1555 1555 2.53 LINK NA NA B 102 O HOH C 241 1555 1555 2.90 LINK NA NA B 103 O3' U5P C 104 1555 1555 2.98 LINK O TYR C 48 NA NA C 102 1555 1555 2.84 LINK NA NA C 102 O3' U5P D 101 1555 1555 2.86 LINK O TYR F 48 NA NA F 103 1555 1555 2.83 CISPEP 1 PRO F 15 ASN F 16 0 -8.32 SITE 1 AC1 6 LYS A 27 LYS A 29 TYR A 71 LYS D 27 SITE 2 AC1 6 LYS D 29 GLU D 70 SITE 1 AC2 5 TYR A 19 ARG A 22 LYS A 26 TYR A 71 SITE 2 AC2 5 SO4 F 102 SITE 1 AC3 5 TYR A 48 LYS A 63 HIS A 64 U5P A 104 SITE 2 AC3 5 U5P B 104 SITE 1 AC4 13 GLU A 18 ASN A 47 TYR A 48 LYS A 63 SITE 2 AC4 13 NA A 103 HOH A 209 HOH A 225 U5P B 104 SITE 3 AC4 13 TYR F 48 PHE F 62 HIS F 64 NA F 103 SITE 4 AC4 13 U5P F 104 SITE 1 AC5 2 LYS B 29 ASP B 39 SITE 1 AC6 5 HOH B 235 U5P C 104 HOH C 213 HOH C 240 SITE 2 AC6 5 HOH C 241 SITE 1 AC7 5 TYR B 48 LYS B 63 HIS B 64 U5P B 104 SITE 2 AC7 5 U5P C 104 SITE 1 AC8 15 TYR A 48 PHE A 62 HIS A 64 NA A 103 SITE 2 AC8 15 U5P A 104 ASN B 47 TYR B 48 LYS B 63 SITE 3 AC8 15 NA B 103 HOH B 209 HOH B 233 HOH B 237 SITE 4 AC8 15 HOH B 239 U5P C 104 HOH C 240 SITE 1 AC9 4 THR B 43 ARG C 22 TYR C 71 HOH C 211 SITE 1 AD1 5 TYR C 48 LYS C 63 HIS C 64 U5P C 104 SITE 2 AD1 5 U5P D 101 SITE 1 AD2 18 TYR B 48 PHE B 62 HIS B 64 NA B 102 SITE 2 AD2 18 NA B 103 U5P B 104 HOH B 207 HOH B 239 SITE 3 AD2 18 GLU C 18 ASN C 47 TYR C 48 LYS C 63 SITE 4 AD2 18 HIS C 64 NA C 102 HOH C 237 HOH C 240 SITE 5 AD2 18 HOH C 241 U5P D 101 SITE 1 AD3 15 HOH B 239 TYR C 48 PHE C 62 HIS C 64 SITE 2 AD3 15 NA C 102 U5P C 104 HOH C 241 GLU D 18 SITE 3 AD3 15 ASN D 47 TYR D 48 LYS D 63 HIS D 64 SITE 4 AD3 15 HOH D 222 HOH D 235 U5P E 104 SITE 1 AD4 9 LYS E 27 LYS E 29 ASP E 39 GLU E 70 SITE 2 AD4 9 TYR E 71 HOH E 205 ASN F 24 LYS F 26 SITE 3 AD4 9 TYR F 71 SITE 1 AD5 8 ASN E 24 LYS E 26 HOH E 203 HOH E 213 SITE 2 AD5 8 HOH E 239 LYS F 27 LYS F 29 HOH F 214 SITE 1 AD6 1 THR E 43 SITE 1 AD7 14 TYR D 48 PHE D 62 HIS D 64 U5P D 101 SITE 2 AD7 14 HOH D 236 GLU E 18 ASN E 47 TYR E 48 SITE 3 AD7 14 PHE E 62 LYS E 63 HIS E 64 HOH E 225 SITE 4 AD7 14 HOH E 245 U5P F 104 SITE 1 AD8 5 GLU F 36 VAL F 37 ARG F 57 HOH F 236 SITE 2 AD8 5 HOH F 244 SITE 1 AD9 4 TYR A 71 SO4 A 102 THR F 43 MET F 51 SITE 1 AE1 5 U5P A 104 TYR F 48 LYS F 63 HIS F 64 SITE 2 AE1 5 U5P F 104 SITE 1 AE2 15 U5P A 104 HOH B 239 TYR E 48 PHE E 62 SITE 2 AE2 15 HIS E 64 U5P E 104 GLU F 18 ASN F 47 SITE 3 AE2 15 TYR F 48 LYS F 63 HIS F 64 NA F 103 SITE 4 AE2 15 HOH F 223 HOH F 226 HOH F 245 CRYST1 57.741 66.874 109.310 90.00 90.00 90.00 P 21 21 21 24 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 0.017319 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009148 0.00000