PDB Short entry for 1C25 HEADER HYDROLASE 17-APR-98 1C25 TITLE HUMAN CDC25A CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDC25A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: M-PHASE INDUCER PHOSPHATASE 1; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 GENE: CDC25A; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET21A; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS HYDROLASE, CELL CYCLE PHOSPHATASE, DUAL SPECIFICITY PROTEIN KEYWDS 2 PHOSPHATASE, CDK2 EXPDTA X-RAY DIFFRACTION AUTHOR E.B.FAUMAN,J.P.COGSWELL,B.LOVEJOY,W.J.ROCQUE,W.HOLMES,V.G.MONTANA, AUTHOR 2 H.PIWNICA-WORMS,M.J.RINK,M.A.SAPER REVDAT 3 07-FEB-24 1C25 1 REMARK REVDAT 2 24-FEB-09 1C25 1 VERSN REVDAT 1 19-AUG-98 1C25 0 JRNL AUTH E.B.FAUMAN,J.P.COGSWELL,B.LOVEJOY,W.J.ROCQUE,W.HOLMES, JRNL AUTH 2 V.G.MONTANA,H.PIWNICA-WORMS,M.J.RINK,M.A.SAPER JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE HUMAN CELL JRNL TITL 2 CYCLE CONTROL PHOSPHATASE, CDC25A. JRNL REF CELL(CAMBRIDGE,MASS.) V. 93 617 1998 JRNL REFN ISSN 0092-8674 JRNL PMID 9604936 JRNL DOI 10.1016/S0092-8674(00)81190-3 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 9429 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) : 0.227 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 467 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 30 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 290 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE : 0.4290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 16 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.107 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1335 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.590 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 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) : 1.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.000 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.900 ; 2.000 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : PARAM11.WAT REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 5.8-7.4 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 : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12551 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : 0.37200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MICROLITERS PROTEIN (10 MG/ML IN 200 REMARK 280 MM NACL, 1 MM DTT, 20 MM HEPES, PH 7.4) MIXED WITH 4 MICROLITERS REMARK 280 WELL BUFFER (18-20% PEG 3350, 0.025% BETA-OCTYLGLUCOSIDE, 0.11 M REMARK 280 SODIUM CITRATE, PH 5.8) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.54800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.27400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.82200 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 377 CG CD CE NZ REMARK 480 LYS A 396 CG CD CE NZ REMARK 480 LYS A 456 CG CD CE NZ REMARK 480 LYS A 470 CG CD CE NZ 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 907 O HOH A 917 2.06 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 PRO A 415 -159.82 -110.26 REMARK 500 ILE A 416 -92.10 66.54 REMARK 500 VAL A 417 172.76 57.70 REMARK 500 PRO A 418 91.38 -67.40 REMARK 500 ASP A 420 12.37 35.22 REMARK 500 CYS A 430 -128.56 -134.39 REMARK 500 GLU A 435 -70.96 82.91 REMARK 500 LYS A 494 33.16 -170.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: DSU REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CYS A 384 AND CYS A 340 MAY FORM DISULFIDE BOND REMARK 800 UNDER CERTAIN CONDITIONS. SEE REFERENCE 1. REMARK 800 REMARK 800 SITE_IDENTIFIER: POP REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PUTATIVE PHOSPHATE BINDING LOOP, CYS-X(5)-ARG REMARK 800 SIGNATURE MOTIF. DBREF 1C25 A 336 495 UNP P30304 MPIP1_HUMAN 336 495 SEQRES 1 A 161 MET LEU ILE GLY ASP PHE SER LYS GLY TYR LEU PHE HIS SEQRES 2 A 161 THR VAL ALA GLY LYS HIS GLN ASP LEU LYS TYR ILE SER SEQRES 3 A 161 PRO GLU ILE MET ALA SER VAL LEU ASN GLY LYS PHE ALA SEQRES 4 A 161 ASN LEU ILE LYS GLU PHE VAL ILE ILE ASP CYS ARG TYR SEQRES 5 A 161 PRO TYR GLU TYR GLU GLY GLY HIS ILE LYS GLY ALA VAL SEQRES 6 A 161 ASN LEU HIS MET GLU GLU GLU VAL GLU ASP PHE LEU LEU SEQRES 7 A 161 LYS LYS PRO ILE VAL PRO THR ASP GLY LYS ARG VAL ILE SEQRES 8 A 161 VAL VAL PHE HIS CYS GLU PHE SER SER GLU ARG GLY PRO SEQRES 9 A 161 ARG MET CYS ARG TYR VAL ARG GLU ARG ASP ARG LEU GLY SEQRES 10 A 161 ASN GLU TYR PRO LYS LEU HIS TYR PRO GLU LEU TYR VAL SEQRES 11 A 161 LEU LYS GLY GLY TYR LYS GLU PHE PHE MET LYS CYS GLN SEQRES 12 A 161 SER TYR CYS GLU PRO PRO SER TYR ARG PRO MET HIS HIS SEQRES 13 A 161 GLU ASP PHE LYS GLU FORMUL 2 HOH *82(H2 O) HELIX 1 1 PRO A 361 LEU A 368 1 8 HELIX 2 2 PRO A 387 GLY A 392 1 6 HELIX 3 3 GLU A 404 PHE A 410 1 7 HELIX 4 4 ARG A 436 LEU A 450 1 15 HELIX 5 5 GLY A 468 LYS A 475 1 8 HELIX 6 6 GLN A 477 TYR A 479 5 3 SHEET 1 A 3 LEU A 462 VAL A 464 0 SHEET 2 A 3 ARG A 423 HIS A 429 1 N VAL A 426 O TYR A 463 SHEET 3 A 3 ILE A 376 ASP A 383 1 N LYS A 377 O ARG A 423 CISPEP 1 TYR A 454 PRO A 455 0 0.58 CISPEP 2 GLU A 481 PRO A 482 0 -0.70 SITE 1 DSU 2 CYS A 430 CYS A 384 SITE 1 POP 7 CYS A 430 GLU A 431 PHE A 432 SER A 433 SITE 2 POP 7 SER A 434 GLU A 435 ARG A 436 CRYST1 43.507 43.507 117.096 90.00 90.00 90.00 P 41 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 0.022985 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008540 0.00000