10 20 30 40 50 60 70 80 2IFD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 20-SEP-06 2IFD
TITLE CRYSTAL STRUCTURE OF A REMOTE BINDING SITE MUTANT, R492L, TITLE 2 OF CDC25B PHOSPHATASE CATALYTIC DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: M-PHASE INDUCER PHOSPHATASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 391-564; COMPND 5 SYNONYM: DUAL SPECIFICITY PHOSPHATASE CDC25B; 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 GENE: CDC25B, CDC25HU2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3
KEYWDS PHOSPHATASE, DUAL SPECIFICITY, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.RUDOLPH,G.BUHRMAN
REVDAT 2 24-FEB-09 2IFD 1 VERSN REVDAT 1 27-FEB-07 2IFD 0
JRNL AUTH J.SOHN,G.BUHRMAN,J.RUDOLPH JRNL TITL KINETIC AND STRUCTURAL STUDIES OF SPECIFIC JRNL TITL 2 PROTEIN-PROTEIN INTERACTIONS IN SUBSTRATE JRNL TITL 3 CATALYSIS BY CDC25B PHOSPHATASE. JRNL REF BIOCHEMISTRY V. 46 807 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17223702 JRNL DOI 10.1021/BI061257Y
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 29.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 201635.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 18160 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) : 0.191 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1783 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) (%) : 93.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2546 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 298 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1488 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.91000 REMARK 3 B22 (A**2) : -2.63000 REMARK 3 B33 (A**2) : -1.28000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.84 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) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 45.31 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.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 2IFD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-06. REMARK 100 THE RCSB ID CODE IS RCSB039512.
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 REMARK 200 PH : 7.5 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) : 1.00 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18160 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.25000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.1000 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 <I/SIGMA(I)> 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 (%): 62.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DTT, AMMONIUM SULFATE, TRIS, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 24.97850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.97850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.66000 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 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 -7.63 79.94 REMARK 500 PRO A 457 134.63 -38.91 REMARK 500 CYS A 473 -140.29 -135.89 REMARK 500 GLU A 478 -62.77 -122.32 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 551 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201 REMARK 800 SITE_IDENTIFIER: AC3 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: 1QB0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CDC25B CATALYTIC DOMAIN REMARK 900 RELATED ID: 2A2K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ACTIVE SITE MUTANT, C473S, OF REMARK 900 CDC25B PHOSPHATASE CATALYTIC DOMAIN REMARK 900 RELATED ID: 2IFV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ACITVE SITE MUTANT, C473D, OF REMARK 900 CDC25B PHOSPHATASE CATALYTIC DOMAIN
DBREF 2IFD A 377 550 UNP P30305 MPIP2_HUMAN 391 564
SEQADV 2IFD MET A 376 UNP P30305 INITIATING METHIONINE SEQADV 2IFD LEU A 492 UNP P30305 ARG 506 ENGINEERED
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 CYS GLU PHE SER SER GLU ARG SEQRES 9 A 175 GLY PRO ARG MET CYS ARG PHE ILE ARG GLU ARG ASP LEU 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
HET SO4 A 551 5 HET CL A 201 1 HET CL A 202 1
HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION
FORMUL 2 SO4 O4 S 2- FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *146(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 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 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
CISPEP 1 TYR A 497 PRO A 498 0 -0.25 CISPEP 2 GLU A 524 PRO A 525 0 -0.40
SITE 1 AC1 9 HOH A 64 HOH A 105 CYS A 473 GLU A 474 SITE 2 AC1 9 PHE A 475 SER A 476 SER A 477 GLU A 478 SITE 3 AC1 9 ARG A 479 SITE 1 AC2 4 HOH A 13 HOH A 65 GLU A 446 ARG A 548 SITE 1 AC3 2 LYS A 394 LYS A 509
CRYST1 49.957 71.320 75.060 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 0.020017 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014021 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013323 0.00000