HEADER HYDROLASE 14-MAR-13 4JMJ TITLE STRUCTURE OF DUSP11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA/RNP COMPLEX-1-INTERACTING PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 28-208; COMPND 5 SYNONYM: DUAL SPECIFICITY PROTEIN PHOSPHATASE 11, PHOSPHATASE THAT COMPND 6 INTERACTS WITH RNA/RNP COMPLEX 1; COMPND 7 EC: 3.1.3.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DUSP11, PIR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALPHA/BETA HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.G.JEONG,S.J.KIM,S.E.RYU REVDAT 3 08-NOV-23 4JMJ 1 REMARK REVDAT 2 25-DEC-19 4JMJ 1 JRNL SEQADV REVDAT 1 26-FEB-14 4JMJ 0 JRNL AUTH D.G.JEONG,C.H.WEI,B.KU,T.J.JEON,P.N.CHIEN,J.K.KIM,S.Y.PARK, JRNL AUTH 2 H.S.HWANG,S.Y.RYU,H.PARK,D.S.KIM,S.J.KIM,S.E.RYU JRNL TITL THE FAMILY-WIDE STRUCTURE AND FUNCTION OF HUMAN JRNL TITL 2 DUAL-SPECIFICITY PROTEIN PHOSPHATASES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 421 2014 JRNL REFN ESSN 1399-0047 JRNL PMID 24531476 JRNL DOI 10.1107/S1399004713029866 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9232 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 496 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 27.3621 - 3.7788 1.00 2235 124 0.1521 0.1797 REMARK 3 2 3.7788 - 3.0006 1.00 2191 117 0.1838 0.2386 REMARK 3 3 3.0006 - 2.6216 0.99 2150 128 0.2305 0.2692 REMARK 3 4 2.6216 - 2.3821 0.99 2160 127 0.2274 0.2958 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.44 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 1547 REMARK 3 ANGLE : 1.152 2093 REMARK 3 CHIRALITY : 0.084 217 REMARK 3 PLANARITY : 0.005 276 REMARK 3 DIHEDRAL : 16.032 594 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 35.9787 11.8223 3.0491 REMARK 3 T TENSOR REMARK 3 T11: 0.4633 T22: 0.2656 REMARK 3 T33: 0.3359 T12: -0.1166 REMARK 3 T13: 0.0506 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.5096 L22: 1.9898 REMARK 3 L33: 2.0453 L12: -0.2733 REMARK 3 L13: 0.1176 L23: 0.3033 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: -0.0697 S13: -0.1367 REMARK 3 S21: 0.0092 S22: -0.1260 S23: 0.2468 REMARK 3 S31: 0.5406 S32: -0.3939 S33: -0.0043 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 4JMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1. REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9276 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1YN9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, HEPES, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.15200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.15200 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.15200 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O HOH A 309 O HOH A 319 2.13 REMARK 500 NH2 ARG A 165 O HOH A 330 2.14 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 PHE A 44 91.31 -163.39 REMARK 500 TYR A 68 -12.88 -143.30 REMARK 500 PRO A 79 79.62 -65.50 REMARK 500 GLU A 80 -131.85 -95.12 REMARK 500 ASN A 114 39.60 -141.59 REMARK 500 SER A 125 -141.95 -113.97 REMARK 500 LEU A 129 -61.73 -125.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 79 GLU A 80 -140.99 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 PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JMK RELATED DB: PDB REMARK 900 RELATED ID: 4KI9 RELATED DB: PDB DBREF 4JMJ A 1 181 UNP O75319 DUS11_HUMAN 28 208 SEQADV 4JMJ SER A 125 UNP O75319 CYS 152 ENGINEERED MUTATION SEQRES 1 A 181 GLY ASN HIS ILE PRO GLU ARG TRP LYS ASP TYR LEU PRO SEQRES 2 A 181 VAL GLY GLN ARG MET PRO GLY THR ARG PHE ILE ALA PHE SEQRES 3 A 181 LYS VAL PRO LEU GLN LYS SER PHE GLU LYS LYS LEU ALA SEQRES 4 A 181 PRO GLU GLU CYS PHE SER PRO LEU ASP LEU PHE ASN LYS SEQRES 5 A 181 ILE ARG GLU GLN ASN GLU GLU LEU GLY LEU ILE ILE ASP SEQRES 6 A 181 LEU THR TYR THR GLN ARG TYR TYR LYS PRO GLU ASP LEU SEQRES 7 A 181 PRO GLU THR VAL PRO TYR LEU LYS ILE PHE THR VAL GLY SEQRES 8 A 181 HIS GLN VAL PRO ASP ASP GLU THR ILE PHE LYS PHE LYS SEQRES 9 A 181 HIS ALA VAL ASN GLY PHE LEU LYS GLU ASN LYS ASP ASN SEQRES 10 A 181 ASP LYS LEU ILE GLY VAL HIS SER THR HIS GLY LEU ASN SEQRES 11 A 181 ARG THR GLY TYR LEU ILE CYS ARG TYR LEU ILE ASP VAL SEQRES 12 A 181 GLU GLY VAL ARG PRO ASP ASP ALA ILE GLU LEU PHE ASN SEQRES 13 A 181 ARG CYS ARG GLY HIS CYS LEU GLU ARG GLN ASN TYR ILE SEQRES 14 A 181 GLU ASP LEU GLN ASN GLY PRO ILE ARG LYS ASN TRP HET PO4 A 201 5 HET CL A 202 1 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 CL CL 1- FORMUL 4 HOH *30(H2 O) HELIX 1 1 ARG A 7 TYR A 11 5 5 HELIX 2 2 GLN A 31 LEU A 38 5 8 HELIX 3 3 SER A 45 GLU A 55 1 11 HELIX 4 4 LYS A 74 LEU A 78 5 5 HELIX 5 5 ASP A 96 GLU A 113 1 18 HELIX 6 6 LEU A 129 GLY A 145 1 17 HELIX 7 7 ARG A 147 GLY A 160 1 14 HELIX 8 8 ARG A 165 GLY A 175 1 11 SHEET 1 A 4 PHE A 23 LYS A 27 0 SHEET 2 A 4 LEU A 120 SER A 125 1 O VAL A 123 N ILE A 24 SHEET 3 A 4 LEU A 60 ASP A 65 1 N GLY A 61 O LEU A 120 SHEET 4 A 4 TYR A 84 LYS A 86 1 O LEU A 85 N ASP A 65 SITE 1 AC1 8 SER A 125 THR A 126 HIS A 127 GLY A 128 SITE 2 AC1 8 LEU A 129 ASN A 130 ARG A 131 HOH A 330 SITE 1 AC2 5 THR A 67 TYR A 68 THR A 69 THR A 126 SITE 2 AC2 5 ARG A 131 CRYST1 94.779 94.779 44.304 90.00 90.00 120.00 P 63 6 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 0.010551 0.006092 0.000000 0.00000 SCALE2 0.000000 0.012183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022571 0.00000