HEADER LYASE 17-DEC-07 3BOB TITLE CARBONIC ANHYDRASE FROM MARINE DIATOM THALASSIOSIRA WEISSFLOGII- TITLE 2 CADMIUM BOUND DOMAIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADMIUM-SPECIFIC CARBONIC ANHYDRASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 2, CDCA1-R2; COMPND 5 EC: 4.2.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THALASSIOSIRA WEISSFLOGII; SOURCE 3 ORGANISM_TAXID: 67004; SOURCE 4 GENE: CDCA1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CARBONIC ANHYDRASE, MARINE DIATOM, CADMIUM-BOUND, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,L.FENG,P.D.JEFFREY,Y.SHI,F.M.M.MOREL REVDAT 5 21-FEB-24 3BOB 1 REMARK LINK REVDAT 4 26-MAY-10 3BOB 1 HEADER COMPND KEYWDS REVDAT 3 24-FEB-09 3BOB 1 VERSN REVDAT 2 18-MAR-08 3BOB 1 JRNL REVDAT 1 22-JAN-08 3BOB 0 JRNL AUTH Y.XU,L.FENG,P.D.JEFFREY,Y.SHI,F.M.MOREL JRNL TITL STRUCTURE AND METAL EXCHANGE IN THE CADMIUM CARBONIC JRNL TITL 2 ANHYDRASE OF MARINE DIATOMS. JRNL REF NATURE V. 452 56 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18322527 JRNL DOI 10.1038/NATURE06636 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1029413.410 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 32511 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) : 0.167 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1615 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4991 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 244 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1568 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.02000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : -2.94000 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) : 0.14 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.000 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) : 2.040 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.510 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.690 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.880 ; 3.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 55.31 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CADMIUM.PARAM REMARK 3 PARAMETER FILE 5 : 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 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045763. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 20% (W/V) REMARK 280 PEG3350, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 32.14150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.10100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.14150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.10100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1203 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1217 LIES ON A SPECIAL POSITION. 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 SER A 223 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 ASP A 321 -131.67 54.02 REMARK 500 GLN A 345 35.72 -94.26 REMARK 500 THR A 370 25.94 -140.42 REMARK 500 ASP A 390 76.49 -156.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 RELATIVE TO THE ORIGINAL COORDINATES THE CADMIUM AND WATER MOLECULE REMARK 600 NUMBERING HAS BEEN OFFSET BY 1000, AND THE CHAIN LABEL HAS BEEN SET REMARK 600 TO THAT OF THE POLYPEPTIDE CHAIN. 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 CD A1001 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 263 SG REMARK 620 2 HIS A 315 NE2 101.6 REMARK 620 3 CYS A 325 SG 126.3 91.8 REMARK 620 4 HOH A1002 O 80.4 159.9 103.1 REMARK 620 5 HOH A1003 O 112.6 85.6 120.1 75.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1001 DBREF 3BOB A 223 432 UNP Q50EL4 Q50EL4_THAWE 197 406 SEQRES 1 A 210 SER ILE SER PRO ALA GLN ILE ALA GLU ALA LEU GLN GLY SEQRES 2 A 210 ARG GLY TRP ASP ALA GLU ILE VAL THR ASP ALA SER MET SEQRES 3 A 210 ALA GLY GLN LEU VAL ASP VAL ARG PRO GLU GLY ILE LEU SEQRES 4 A 210 LYS CYS VAL ASP GLY ARG GLY SER ASP ASN THR ARG MET SEQRES 5 A 210 GLY GLY PRO LYS MET PRO GLY GLY ILE TYR ALA ILE ALA SEQRES 6 A 210 HIS ASN ARG GLY VAL THR SER ILE GLU GLY LEU LYS GLN SEQRES 7 A 210 ILE THR LYS GLU VAL ALA SER LYS GLY HIS LEU PRO SER SEQRES 8 A 210 VAL HIS GLY ASP HIS SER SER ASP MET LEU GLY CYS GLY SEQRES 9 A 210 PHE PHE LYS LEU TRP VAL THR GLY ARG PHE ASP ASP MET SEQRES 10 A 210 GLY TYR PRO ARG PRO GLN PHE ASP ALA ASP GLN GLY ALA SEQRES 11 A 210 ASN ALA VAL LYS ASP ALA GLY GLY ILE ILE GLU MET HIS SEQRES 12 A 210 HIS GLY SER HIS THR GLU LYS VAL VAL TYR ILE ASN LEU SEQRES 13 A 210 LEU ALA ASN LYS THR LEU GLU PRO ASN GLU ASN ASP GLN SEQRES 14 A 210 ARG PHE ILE VAL ASP GLY TRP ALA ALA ASP LYS PHE GLY SEQRES 15 A 210 LEU ASP VAL PRO LYS PHE LEU ILE ALA ALA ALA ALA THR SEQRES 16 A 210 VAL GLU MET LEU GLY GLY PRO LYS ASN ALA LYS ILE VAL SEQRES 17 A 210 VAL PRO HET CD A1001 1 HETNAM CD CADMIUM ION FORMUL 2 CD CD 2+ FORMUL 3 HOH *250(H2 O) HELIX 1 1 SER A 225 GLY A 235 1 11 HELIX 2 2 ALA A 246 ALA A 249 5 4 HELIX 3 3 ILE A 283 GLY A 291 1 9 HELIX 4 4 SER A 294 SER A 307 1 14 HELIX 5 5 SER A 320 GLY A 324 5 5 HELIX 6 6 CYS A 325 THR A 333 1 9 HELIX 7 7 PHE A 336 GLY A 340 5 5 HELIX 8 8 ASP A 347 ALA A 358 1 12 HELIX 9 9 GLY A 397 PHE A 403 1 7 HELIX 10 10 ASP A 406 LEU A 421 1 16 SHEET 1 A 4 ASP A 239 THR A 244 0 SHEET 2 A 4 ASN A 426 VAL A 431 1 O ILE A 429 N GLU A 241 SHEET 3 A 4 VAL A 374 ASN A 377 1 N ILE A 376 O LYS A 428 SHEET 4 A 4 PHE A 393 ASP A 396 1 O PHE A 393 N TYR A 375 SHEET 1 B 2 VAL A 253 ASP A 254 0 SHEET 2 B 2 LYS A 382 THR A 383 -1 O THR A 383 N VAL A 253 SHEET 1 C 3 ILE A 260 LEU A 261 0 SHEET 2 C 3 LEU A 311 ASP A 317 1 O LEU A 311 N LEU A 261 SHEET 3 C 3 ILE A 361 HIS A 365 1 O ILE A 361 N PRO A 312 LINK SG CYS A 263 CD CD A1001 1555 1555 2.46 LINK NE2 HIS A 315 CD CD A1001 1555 1555 2.34 LINK SG CYS A 325 CD CD A1001 1555 1555 2.51 LINK CD CD A1001 O HOH A1002 1555 1555 2.65 LINK CD CD A1001 O HOH A1003 1555 1555 2.35 SITE 1 AC1 5 CYS A 263 HIS A 315 CYS A 325 HOH A1002 SITE 2 AC1 5 HOH A1003 CRYST1 64.283 78.202 37.054 90.00 90.00 90.00 P 21 21 2 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 0.015556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026988 0.00000