10 20 30 40 50 60 70 80 1TCA - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE(CARBOXYLIC ESTERASE) 28-FEB-94 1TCA
TITLE THE SEQUENCE, CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT OF TWO TITLE 2 CRYSTAL FORMS OF LIPASE B FROM CANDIDA ANTARCTICA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.3; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ANTARCTICA; SOURCE 3 ORGANISM_COMMON: ASCOMYCETES; SOURCE 4 ORGANISM_TAXID: 34362
KEYWDS HYDROLASE(CARBOXYLIC ESTERASE)
EXPDTA X-RAY DIFFRACTION
AUTHOR J.UPPENBERG,T.A.JONES
REVDAT 4 13-JUL-11 1TCA 1 VERSN REVDAT 3 25-AUG-09 1TCA 1 SOURCE REVDAT 2 24-FEB-09 1TCA 1 VERSN REVDAT 1 31-MAY-94 1TCA 0
JRNL AUTH J.UPPENBERG,M.T.HANSEN,S.PATKAR,T.A.JONES JRNL TITL THE SEQUENCE, CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT JRNL TITL 2 OF TWO CRYSTAL FORMS OF LIPASE B FROM CANDIDA ANTARCTICA. JRNL REF STRUCTURE V. 2 293 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 8087556 JRNL DOI 10.1016/S0969-2126(00)00031-9
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.UPPENBERG,S.PATKAR,T.BERGFORS,T.A.JONES REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF LIPASE B REMARK 1 TITL 2 FROM CANDIDA ANTARCTICA REMARK 1 REF J.MOL.BIOL. V. 235 790 1994 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 37486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1TCA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 31.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.35000 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 ASN A 51 -91.12 -144.18 REMARK 500 ASP A 75 119.60 -33.66 REMARK 500 SER A 105 -126.73 52.70 REMARK 500 ASP A 134 67.36 -114.45 REMARK 500 ASN A 206 -4.18 74.36 REMARK 500 ALA A 305 33.97 -142.89 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 628 DISTANCE = 5.71 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 402
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TCB RELATED DB: PDB REMARK 900 RELATED ID: 1TCC RELATED DB: PDB
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM REMARK 999 THE DNA SEQUENCE OF J.UPPENBERG ET AL., 1994, LISTED IN REMARK 999 THE JRNL REFERENCE ABOVE.
DBREF 1TCA A 1 317 UNP P41365 LIPB_CANAR 26 342
SEQRES 1 A 317 LEU PRO SER GLY SER ASP PRO ALA PHE SER GLN PRO LYS SEQRES 2 A 317 SER VAL LEU ASP ALA GLY LEU THR CYS GLN GLY ALA SER SEQRES 3 A 317 PRO SER SER VAL SER LYS PRO ILE LEU LEU VAL PRO GLY SEQRES 4 A 317 THR GLY THR THR GLY PRO GLN SER PHE ASP SER ASN TRP SEQRES 5 A 317 ILE PRO LEU SER THR GLN LEU GLY TYR THR PRO CYS TRP SEQRES 6 A 317 ILE SER PRO PRO PRO PHE MET LEU ASN ASP THR GLN VAL SEQRES 7 A 317 ASN THR GLU TYR MET VAL ASN ALA ILE THR ALA LEU TYR SEQRES 8 A 317 ALA GLY SER GLY ASN ASN LYS LEU PRO VAL LEU THR TRP SEQRES 9 A 317 SER GLN GLY GLY LEU VAL ALA GLN TRP GLY LEU THR PHE SEQRES 10 A 317 PHE PRO SER ILE ARG SER LYS VAL ASP ARG LEU MET ALA SEQRES 11 A 317 PHE ALA PRO ASP TYR LYS GLY THR VAL LEU ALA GLY PRO SEQRES 12 A 317 LEU ASP ALA LEU ALA VAL SER ALA PRO SER VAL TRP GLN SEQRES 13 A 317 GLN THR THR GLY SER ALA LEU THR THR ALA LEU ARG ASN SEQRES 14 A 317 ALA GLY GLY LEU THR GLN ILE VAL PRO THR THR ASN LEU SEQRES 15 A 317 TYR SER ALA THR ASP GLU ILE VAL GLN PRO GLN VAL SER SEQRES 16 A 317 ASN SER PRO LEU ASP SER SER TYR LEU PHE ASN GLY LYS SEQRES 17 A 317 ASN VAL GLN ALA GLN ALA VAL CYS GLY PRO LEU PHE VAL SEQRES 18 A 317 ILE ASP HIS ALA GLY SER LEU THR SER GLN PHE SER TYR SEQRES 19 A 317 VAL VAL GLY ARG SER ALA LEU ARG SER THR THR GLY GLN SEQRES 20 A 317 ALA ARG SER ALA ASP TYR GLY ILE THR ASP CYS ASN PRO SEQRES 21 A 317 LEU PRO ALA ASN ASP LEU THR PRO GLU GLN LYS VAL ALA SEQRES 22 A 317 ALA ALA ALA LEU LEU ALA PRO ALA ALA ALA ALA ILE VAL SEQRES 23 A 317 ALA GLY PRO LYS GLN ASN CYS GLU PRO ASP LEU MET PRO SEQRES 24 A 317 TYR ALA ARG PRO PHE ALA VAL GLY LYS ARG THR CYS SER SEQRES 25 A 317 GLY ILE VAL THR PRO
MODRES 1TCA ASN A 74 ASN GLYCOSYLATION SITE
HET NAG A 401 14 HET NAG A 402 14
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 HOH *286(H2 O)
HELIX 1 A1 LYS A 13 ALA A 18 1 6 HELIX 2 A2 GLY A 44 THR A 57 1 14 HELIX 3 A3 THR A 76 GLY A 93 1 18 HELIX 4 A4 GLN A 106 PHE A 117 1 12 HELIX 5 A5 GLY A 142 ALA A 146 1 5 HELIX 6 A6 PRO A 152 GLN A 156 1 5 HELIX 7 A7 ALA A 162 ASN A 169 1 8 HELIX 8 A8 ALA A 212 CYS A 216 1 5 HELIX 9 A9 GLY A 226 ARG A 242 1 17 HELIX 10 A10 PRO A 268 ALA A 287 1 20 HELIX 11 TH1 PRO A 119 ILE A 121 5 3 HELIX 12 TH2 VAL A 139 ALA A 141 5 3 HELIX 13 TH3 SER A 250 ASP A 252 5 3 HELIX 14 TH4 ILE A 255 ASP A 257 5 3 HELIX 15 TH5 ARG A 302 PHE A 304 5 3 HELIX 16 P1 PRO A 68 PRO A 70 10 3
SHEET 1 S1 7 LEU A 20 CYS A 22 0 SHEET 2 S1 7 THR A 62 ILE A 66 -1 SHEET 3 S1 7 PRO A 33 VAL A 37 1 SHEET 4 S1 7 LEU A 99 TRP A 104 1 SHEET 5 S1 7 VAL A 125 PHE A 131 1 SHEET 6 S1 7 THR A 179 TYR A 183 1 SHEET 7 S1 7 LYS A 208 GLN A 211 1 SHEET 1 S2 2 ARG A 309 THR A 310 0 SHEET 2 S2 2 GLY A 313 ILE A 314 -1
SSBOND 1 CYS A 22 CYS A 64 1555 1555 2.03 SSBOND 2 CYS A 216 CYS A 258 1555 1555 2.03 SSBOND 3 CYS A 293 CYS A 311 1555 1555 2.04
LINK ND2 ASN A 74 C1 NAG A 401 1555 1555 1.45 LINK O4 NAG A 401 C1 NAG A 402 1555 1555 1.44
CISPEP 1 PRO A 69 PRO A 70 0 -3.77 CISPEP 2 GLN A 191 PRO A 192 0 0.54
SITE 1 CAT 3 SER A 105 ASP A 187 HIS A 224 SITE 1 AC1 8 GLN A 11 ASN A 74 ASP A 75 VAL A 78 SITE 2 AC1 8 NAG A 402 HOH A 436 HOH A 515 HOH A 567 SITE 1 AC2 3 SER A 10 NAG A 401 HOH A 674
CRYST1 62.100 46.700 92.100 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 0.016103 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021413 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010858 0.00000