HEADER HYDROLASE 26-AUG-99 1CWR TITLE HUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (M-PHASE INDUCER PHOSPHATASE 2 (CDC25B)); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 EC: 3.1.3.48; 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 EXPDTA X-RAY DIFFRACTION AUTHOR K.D.WATENPAUGH,R.A.REYNOLDS,C.G.CHIDESTER REVDAT 4 06-DEC-23 1CWR 1 REMARK LINK REVDAT 3 24-FEB-09 1CWR 1 VERSN REVDAT 2 01-APR-03 1CWR 1 JRNL REVDAT 1 28-AUG-00 1CWR 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.204 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) : 14723 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.172 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 594 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10870 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 : 9 REMARK 3 SOLVENT ATOMS : 103 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 : 3 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) : 0.030 REMARK 3 ANGLE DISTANCES (A) : 0.200 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: REMARK 3 RESIDUES CYS A 426, CYS A 474; AND ARG A 479 EACH REMARK 3 HAVE TWO ALTERNATIVE CONFORMATIONS MODELED. REMARK 3 CYS 426 AND CYS 473 FORM A DISULFIDE APROXIMATELY REMARK 3 50 PERCENT OF THE TIME. REMARK 4 REMARK 4 1CWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-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 : SAINT, SADIE REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 80.4 REMARK 200 DATA REDUNDANCY : 1.750 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 (%): 55.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MICROLITERS PROTEIN (10 MG/ ML IN 50 REMARK 280 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL REMARK 280 BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 REMARK 280 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 25.86650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.62350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.62350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.86650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.55500 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 VAL A 356 REMARK 465 LEU A 357 REMARK 465 ARG A 358 REMARK 465 SER A 359 REMARK 465 LYS A 360 REMARK 465 SER A 361 REMARK 465 LEU A 362 REMARK 465 CYS A 363 REMARK 465 HIS A 364 REMARK 465 ASP A 365 REMARK 465 GLU A 366 REMARK 465 ILE A 367 REMARK 465 GLU A 368 REMARK 465 ASN A 369 REMARK 465 LEU A 370 REMARK 465 LEU A 371 REMARK 465 ASP A 372 REMARK 465 SER A 373 REMARK 465 GLY A 552 REMARK 465 GLU A 553 REMARK 465 ARG A 554 REMARK 465 SER A 555 REMARK 465 ARG A 556 REMARK 465 ARG A 557 REMARK 465 GLU A 558 REMARK 465 LEU A 559 REMARK 465 CYS A 560 REMARK 465 SER A 561 REMARK 465 ARG A 562 REMARK 465 LEU A 563 REMARK 465 GLN A 564 REMARK 465 ASP A 565 REMARK 465 GLN A 566 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 CYS A 426 CA - CB - SG ANGL. DEV. = 10.2 DEGREES REMARK 500 CYS A 473 CB - CA - C ANGL. DEV. = 7.4 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 -8.60 81.51 REMARK 500 CYS A 473 -146.24 -122.52 REMARK 500 SER A 476 58.14 38.01 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 SO4 A 567 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QB0 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN CDC25B DBREF 1CWR A 356 566 UNP P30305 MPIP2_HUMAN 356 566 SEQRES 1 A 211 VAL LEU ARG SER LYS SER LEU CYS HIS ASP GLU ILE GLU SEQRES 2 A 211 ASN LEU LEU ASP SER ASP HIS ARG GLU LEU ILE GLY ASP SEQRES 3 A 211 TYR SER LYS ALA PHE LEU LEU GLN THR VAL ASP GLY LYS SEQRES 4 A 211 HIS GLN ASP LEU LYS TYR ILE SER PRO GLU THR MET VAL SEQRES 5 A 211 ALA LEU LEU THR GLY LYS PHE SER ASN ILE VAL ASP LYS SEQRES 6 A 211 PHE VAL ILE VAL ASP CYS ARG TYR PRO TYR GLU TYR GLU SEQRES 7 A 211 GLY GLY HIS ILE LYS THR ALA VAL ASN LEU PRO LEU GLU SEQRES 8 A 211 ARG ASP ALA GLU SER PHE LEU LEU LYS SER PRO ILE ALA SEQRES 9 A 211 PRO CYS SER LEU ASP LYS ARG VAL ILE LEU ILE PHE HIS SEQRES 10 A 211 CYS GLU PHE SER SER GLU ARG GLY PRO ARG MET CYS ARG SEQRES 11 A 211 PHE ILE ARG GLU ARG ASP ARG ALA VAL ASN ASP TYR PRO SEQRES 12 A 211 SER LEU TYR TYR PRO GLU MET TYR ILE LEU LYS GLY GLY SEQRES 13 A 211 TYR LYS GLU PHE PHE PRO GLN HIS PRO ASN PHE CYS GLU SEQRES 14 A 211 PRO GLN ASP TYR ARG PRO MET ASN HIS GLU ALA PHE LYS SEQRES 15 A 211 ASP GLU LEU LYS THR PHE ARG LEU LYS THR ARG SER TRP SEQRES 16 A 211 ALA GLY GLU ARG SER ARG ARG GLU LEU CYS SER ARG LEU SEQRES 17 A 211 GLN ASP GLN HET SO4 A 567 5 HET BME A 4 4 HETNAM SO4 SULFATE ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 SO4 O4 S 2- FORMUL 3 BME C2 H6 O S FORMUL 4 HOH *103(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 SSBOND 1 CYS A 426 CYS A 473 1555 1555 1.96 LINK S2 BME A 4 SG CYS A 484 1555 1555 1.97 CISPEP 1 TYR A 497 PRO A 498 0 -0.87 CISPEP 2 GLU A 524 PRO A 525 0 -9.65 SITE 1 AC1 5 ARG A 488 ARG A 492 HOH A 616 HOH A 644 SITE 2 AC1 5 HOH A 660 SITE 1 AC2 4 CYS A 484 MET A 505 HOH A 590 HOH A 613 CRYST1 51.733 71.110 75.247 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 0.019330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013290 0.00000