HEADER CELL CYCLE 26-AUG-99 1CWT TITLE HUMAN CDC25B CATALYTIC DOMAIN WITH METHYL MERCURY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDC25 B-TYPE TYROSINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: M-PHASE INDUCER PHOSPHATASE 2 (CDC25B); 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 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: CDC25B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: XL1-BLUE KEYWDS HYDROLASE, CELL CYCLE PHOSPHATASE, DUAL SPECIFICITY PROTEIN KEYWDS 2 PHOSPHATASE, CDC25, CDC25B, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.WATENPAUGH,R.A.REYNOLDS REVDAT 4 07-FEB-24 1CWT 1 REMARK LINK REVDAT 3 24-FEB-09 1CWT 1 VERSN REVDAT 2 01-APR-03 1CWT 1 JRNL REVDAT 1 30-AUG-00 1CWT 0 JRNL AUTH R.A.REYNOLDS,A.W.YEM,C.L.WOLFE,M.R.DEIBEL JR.,C.G.CHIDESTER, JRNL AUTH 2 K.D.WATENPAUGH JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF CDC25B JRNL TITL 2 REQUIRED FOR G2/M PHASE TRANSITION OF THE CELL CYCLE. JRNL REF J.MOL.BIOL. V. 293 559 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10543950 JRNL DOI 10.1006/JMBI.1999.3168 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.168 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11361 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.146 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 472 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8778 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SADIE REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17378 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 1.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31000 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: MIR REMARK 200 SOFTWARE USED: XTAL V. 3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MICROLITERS PROTEIN (10 MG/ ML IN 50 REMARK 280 MM TRISHCL, CH(3)HGCL,1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS REMARK 280 WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) REMARK 280 AT 4 DEG. C 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 26.08300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.77650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.18900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.77650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.08300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.18900 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 551 CA C O CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 488 CD - NE - CZ ANGL. DEV. = 8.4 DEGREES 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 THR A 439 -15.11 88.33 REMARK 500 CYS A 473 -136.52 -133.75 REMARK 500 GLU A 478 -61.91 -125.72 REMARK 500 TRP A 550 -86.60 -124.77 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 MMC A 4 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 484 SG REMARK 620 2 MMC A 4 C 163.5 REMARK 620 3 CYS A 484 O 80.6 111.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 552 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 553 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMC A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QB0 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF HUMAN CDC25B CATALYTIC DOMAIN REMARK 900 RELATED ID: 1CWR RELATED DB: PDB REMARK 900 ROOM TEMPERATURE STRUCTURE OF THE HUMAN CDC25B CATALYTIC DOMAIN REMARK 900 WITHOUT OXYANION IN ACTIVE SITE. REMARK 900 RELATED ID: 1CWS RELATED DB: PDB REMARK 900 ROOM TEMPERATURE STRUCTURE OF THE HUMAN CDC25B CATALYTIC DOMAIN REMARK 900 WITH TUNGSTATE IN ACTIVE SITE. DBREF 1CWT A 374 551 UNP P30305 MPIP2_HUMAN 347 524 SEQRES 1 A 178 ASP HIS ARG GLU LEU ILE GLY ASP TYR SER LYS ALA PHE SEQRES 2 A 178 LEU LEU GLN THR VAL ASP GLY LYS HIS GLN ASP LEU LYS SEQRES 3 A 178 TYR ILE SER PRO GLU THR MET VAL ALA LEU LEU THR GLY SEQRES 4 A 178 LYS PHE SER ASN ILE VAL ASP LYS PHE VAL ILE VAL ASP SEQRES 5 A 178 CYS ARG TYR PRO TYR GLU TYR GLU GLY GLY HIS ILE LYS SEQRES 6 A 178 THR ALA VAL ASN LEU PRO LEU GLU ARG ASP ALA GLU SER SEQRES 7 A 178 PHE LEU LEU LYS SER PRO ILE ALA PRO CYS SER LEU ASP SEQRES 8 A 178 LYS ARG VAL ILE LEU ILE PHE HIS CYS GLU PHE SER SER SEQRES 9 A 178 GLU ARG GLY PRO ARG MET CYS ARG PHE ILE ARG GLU ARG SEQRES 10 A 178 ASP ARG ALA VAL ASN ASP TYR PRO SER LEU TYR TYR PRO SEQRES 11 A 178 GLU MET TYR ILE LEU LYS GLY GLY TYR LYS GLU PHE PHE SEQRES 12 A 178 PRO GLN HIS PRO ASN PHE CYS GLU PRO GLN ASP TYR ARG SEQRES 13 A 178 PRO MET ASN HIS GLU ALA PHE LYS ASP GLU LEU LYS THR SEQRES 14 A 178 PHE ARG LEU LYS THR ARG SER TRP ALA HET SO4 A 552 5 HET SO4 A 553 5 HET CL A 554 1 HET MMC A 4 2 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM MMC METHYL MERCURY ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 CL CL 1- FORMUL 5 MMC C H3 HG 1+ FORMUL 6 HOH *130(H2 O) HELIX 1 1 ILE A 401 THR A 411 1 11 HELIX 2 2 PRO A 429 GLY A 434 1 6 HELIX 3 3 GLU A 446 LEU A 454 1 9 HELIX 4 4 GLU A 478 VAL A 494 1 17 HELIX 5 5 GLY A 511 PHE A 515 1 5 HELIX 6 6 GLU A 534 LYS A 546 1 13 SHEET 1 A 5 TYR A 400 ILE A 401 0 SHEET 2 A 5 MET A 505 LEU A 508 1 O ILE A 507 N ILE A 401 SHEET 3 A 5 ARG A 466 HIS A 472 1 O LEU A 469 N TYR A 506 SHEET 4 A 5 VAL A 418 ASP A 425 1 N ASP A 419 O ARG A 466 SHEET 5 A 5 VAL A 441 ASN A 442 1 O VAL A 441 N ASP A 425 SHEET 1 B 2 HIS A 436 ILE A 437 0 SHEET 2 B 2 CYS A 523 GLU A 524 -1 N GLU A 524 O HIS A 436 LINK HG MMC A 4 SG CYS A 484 1555 1555 2.30 LINK HG MMC A 4 O CYS A 484 1555 1555 3.30 CISPEP 1 TYR A 497 PRO A 498 0 1.25 CISPEP 2 GLU A 524 PRO A 525 0 -3.84 SITE 1 AC1 10 CYS A 473 GLU A 474 PHE A 475 SER A 476 SITE 2 AC1 10 SER A 477 GLU A 478 ARG A 479 HOH A 585 SITE 3 AC1 10 HOH A 624 HOH A 673 SITE 1 AC2 4 ARG A 488 ARG A 492 HOH A 598 HOH A 614 SITE 1 AC3 3 GLU A 446 ARG A 548 HOH A 579 SITE 1 AC4 3 LEU A 398 CYS A 484 MET A 505 CRYST1 52.166 72.378 75.553 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 0.019170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013236 0.00000