HEADER HYDROLASE, CELL CYCLE 20-JAN-05 1YM9 TITLE CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH THE TITLE 2 ACTIVE SITE CYSTEINE IN THE SULFINIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: M-PHASE INDUCER PHOSPHATASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: CDC25B PHOSPHATASE; DUAL SPECIFICITY PHOSPHATASE CDC25B; COMPND 6 EC: 3.1.3.48; COMPND 7 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: CDC25B, CDC25HU2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SULFINIC CYSTEINE, HYDROLASE, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR G.K.BUHRMAN,B.PARKER,J.SOHN,J.RUDOLPH,C.MATTOS REVDAT 5 23-AUG-23 1YM9 1 REMARK SEQADV LINK REVDAT 4 31-JAN-18 1YM9 1 REMARK REVDAT 3 12-NOV-14 1YM9 1 HET HETATM HETNAM HETSYN REVDAT 3 2 1 LINK MODRES SEQRES VERSN REVDAT 2 24-FEB-09 1YM9 1 VERSN REVDAT 1 12-APR-05 1YM9 0 JRNL AUTH G.K.BUHRMAN,B.PARKER,J.SOHN,J.RUDOLPH,C.MATTOS JRNL TITL STRUCTURAL MECHANISM OF OXIDATIVE REGULATION OF THE JRNL TITL 2 PHOSPHATASE CDC25B VIA AN INTRAMOLECULAR DISULFIDE BOND JRNL REF BIOCHEMISTRY V. 44 5307 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15807524 JRNL DOI 10.1021/BI047449FS0006-2960(04)07449-5 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 431894.490 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 16387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1626 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2319 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 254 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1429 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.30000 REMARK 3 B22 (A**2) : -2.13000 REMARK 3 B33 (A**2) : -2.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.580 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.080 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.130 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 19.44 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN3.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN3.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031680. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16387 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1QB0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DTT, TRIS, AMMONIUM SULFATE, PH 7.25, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100.0K 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 24.63400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.88050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.31350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.88050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.63400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.31350 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: 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 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 CYS A 461 REMARK 465 SER A 462 REMARK 465 LEU A 463 REMARK 465 ASP A 464 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 THR A 439 -3.44 79.45 REMARK 500 CSD A 473 -144.95 -128.15 REMARK 500 PHE A 475 -106.12 -126.78 REMARK 500 ASN A 532 34.81 -93.12 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 CL A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YMD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH REMARK 900 THE ACTIVE SITE CYSTEINE IN THE SULFONIC FORM REMARK 900 RELATED ID: 1YMK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN IN THE REMARK 900 APO FORM REMARK 900 RELATED ID: 1YML RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH REMARK 900 THE ACTIVE SITE CYSTEINE IN THE SULFENIC FORM REMARK 900 RELATED ID: 1YS0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH REMARK 900 THE ACTIVE SITE CYSTEINE IN THE DISULFIDE FORM DBREF 1YM9 A 377 550 UNP P30305 MPIP2_HUMAN 391 564 SEQADV 1YM9 MET A 376 UNP P30305 INITIATING METHIONINE SEQADV 1YM9 CSD A 473 UNP P30305 CYS 487 MODIFIED RESIDUE SEQRES 1 A 175 MET GLU LEU ILE GLY ASP TYR SER LYS ALA PHE LEU LEU SEQRES 2 A 175 GLN THR VAL ASP GLY LYS HIS GLN ASP LEU LYS TYR ILE SEQRES 3 A 175 SER PRO GLU THR MET VAL ALA LEU LEU THR GLY LYS PHE SEQRES 4 A 175 SER ASN ILE VAL ASP LYS PHE VAL ILE VAL ASP CYS ARG SEQRES 5 A 175 TYR PRO TYR GLU TYR GLU GLY GLY HIS ILE LYS THR ALA SEQRES 6 A 175 VAL ASN LEU PRO LEU GLU ARG ASP ALA GLU SER PHE LEU SEQRES 7 A 175 LEU LYS SER PRO ILE ALA PRO CYS SER LEU ASP LYS ARG SEQRES 8 A 175 VAL ILE LEU ILE PHE HIS CSD GLU PHE SER SER GLU ARG SEQRES 9 A 175 GLY PRO ARG MET CYS ARG PHE ILE ARG GLU ARG ASP ARG SEQRES 10 A 175 ALA VAL ASN ASP TYR PRO SER LEU TYR TYR PRO GLU MET SEQRES 11 A 175 TYR ILE LEU LYS GLY GLY TYR LYS GLU PHE PHE PRO GLN SEQRES 12 A 175 HIS PRO ASN PHE CYS GLU PRO GLN ASP TYR ARG PRO MET SEQRES 13 A 175 ASN HIS GLU ALA PHE LYS ASP GLU LEU LYS THR PHE ARG SEQRES 14 A 175 LEU LYS THR ARG SER TRP MODRES 1YM9 CSD A 473 CYS 3-SULFINOALANINE HET CSD A 473 8 HET CL A1001 1 HETNAM CSD 3-SULFINOALANINE HETNAM CL CHLORIDE ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 CL CL 1- FORMUL 3 HOH *137(H2 O) HELIX 1 1 SER A 402 THR A 411 1 10 HELIX 2 2 TYR A 428 GLY A 434 1 7 HELIX 3 3 LEU A 445 LYS A 455 1 11 HELIX 4 4 GLU A 478 VAL A 494 1 17 HELIX 5 5 GLY A 510 PHE A 516 1 7 HELIX 6 6 HIS A 519 ASN A 521 5 3 HELIX 7 7 HIS A 533 ALA A 535 5 3 HELIX 8 8 PHE A 536 LEU A 545 1 10 SHEET 1 A 5 TYR A 400 ILE A 401 0 SHEET 2 A 5 GLU A 504 LEU A 508 1 O ILE A 507 N ILE A 401 SHEET 3 A 5 ARG A 466 HIS A 472 1 N PHE A 471 O TYR A 506 SHEET 4 A 5 VAL A 418 ASP A 425 1 N VAL A 424 O ILE A 470 SHEET 5 A 5 VAL A 441 ASN A 442 1 O VAL A 441 N ILE A 423 SHEET 1 B 2 HIS A 436 ILE A 437 0 SHEET 2 B 2 CYS A 523 GLU A 524 -1 O GLU A 524 N HIS A 436 LINK C HIS A 472 N CSD A 473 1555 1555 1.33 LINK C CSD A 473 N GLU A 474 1555 1555 1.33 CISPEP 1 TYR A 497 PRO A 498 0 -0.16 CISPEP 2 GLU A 524 PRO A 525 0 -1.01 SITE 1 AC1 4 HOH A 13 HOH A 134 GLU A 446 ARG A 548 CRYST1 49.268 70.627 73.761 90.00 90.00 90.00 P 21 21 21 4 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 0.020297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013557 0.00000