HEADER HYDROLASE 08-SEP-16 5LUJ TITLE STRUCTURE OF CUTINASE 2 FROM THERMOBIFIDA CELLULOSILYTICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CUTINASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CUTINASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOBIFIDA CELLULOSILYTICA; SOURCE 3 ORGANISM_TAXID: 144786; SOURCE 4 GENE: CUT2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET26B(+) KEYWDS CUTINASE, ALPHA/BETA HYDROLASE, POLY(ETHYLENETEREPHTHLATE) (PET), KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.HROMIC,A.LYSKOWSKI,K.GRUBER REVDAT 4 17-JAN-24 5LUJ 1 REMARK REVDAT 3 04-OCT-17 5LUJ 1 JRNL REVDAT 2 09-AUG-17 5LUJ 1 JRNL REVDAT 1 12-JUL-17 5LUJ 0 JRNL AUTH D.RIBITSCH,A.HROMIC,S.ZITZENBACHER,B.ZARTL,C.GAMERITH, JRNL AUTH 2 A.PELLIS,A.JUNGBAUER,A.YSKOWSKI,G.STEINKELLNER,K.GRUBER, JRNL AUTH 3 R.TSCHELIESSNIG,E.HERRERO ACERO,G.M.GUEBITZ JRNL TITL SMALL CAUSE, LARGE EFFECT: STRUCTURAL CHARACTERIZATION OF JRNL TITL 2 CUTINASES FROM THERMOBIFIDA CELLULOSILYTICA. JRNL REF BIOTECHNOL. BIOENG. V. 114 2481 2017 JRNL REFN ESSN 1097-0290 JRNL PMID 28671263 JRNL DOI 10.1002/BIT.26372 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12953 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.5243 - 3.7613 1.00 2598 136 0.1612 0.2043 REMARK 3 2 3.7613 - 2.9857 1.00 2462 133 0.1966 0.2663 REMARK 3 3 2.9857 - 2.6084 1.00 2440 109 0.2073 0.2714 REMARK 3 4 2.6084 - 2.3699 1.00 2413 134 0.1877 0.2375 REMARK 3 5 2.3699 - 2.2001 1.00 2402 126 0.1679 0.2479 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.250 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2001 REMARK 3 ANGLE : 0.786 2730 REMARK 3 CHIRALITY : 0.051 300 REMARK 3 PLANARITY : 0.006 359 REMARK 3 DIHEDRAL : 9.288 1192 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12953 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 43.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1JFR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE AND 30% REMARK 280 W/V PEG MONOMETHYL ETHER 2000, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.17500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.57500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.17500 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 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 CL CL A 301 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 MET A 1 REMARK 465 ARG A 246 REMARK 465 ASP A 247 REMARK 465 GLY A 248 REMARK 465 LEU A 249 REMARK 465 PHE A 250 REMARK 465 GLY A 251 REMARK 465 GLU A 252 REMARK 465 ALA A 263 REMARK 465 LEU A 264 REMARK 465 GLU A 265 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 447 O HOH A 450 3557 1.86 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 ASN A 50 -178.40 -171.26 REMARK 500 THR A 62 12.64 59.38 REMARK 500 SER A 131 -114.87 60.47 REMARK 500 THR A 154 60.66 28.60 REMARK 500 HIS A 185 -82.46 -127.71 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 CL A 301 DBREF 5LUJ A 1 262 UNP E9LVH9 E9LVH9_9ACTN 1 262 SEQADV 5LUJ ALA A 263 UNP E9LVH9 EXPRESSION TAG SEQADV 5LUJ LEU A 264 UNP E9LVH9 EXPRESSION TAG SEQADV 5LUJ GLU A 265 UNP E9LVH9 EXPRESSION TAG SEQRES 1 A 265 MET ALA ASN PRO TYR GLU ARG GLY PRO ASN PRO THR ASP SEQRES 2 A 265 ALA LEU LEU GLU ALA ARG SER GLY PRO PHE SER VAL SER SEQRES 3 A 265 GLU GLU ARG ALA SER ARG PHE GLY ALA ASP GLY PHE GLY SEQRES 4 A 265 GLY GLY THR ILE TYR TYR PRO ARG GLU ASN ASN THR TYR SEQRES 5 A 265 GLY ALA VAL ALA ILE SER PRO GLY TYR THR GLY THR GLN SEQRES 6 A 265 ALA SER VAL ALA TRP LEU GLY GLU ARG ILE ALA SER HIS SEQRES 7 A 265 GLY PHE VAL VAL ILE THR ILE ASP THR ASN THR THR LEU SEQRES 8 A 265 ASP GLN PRO ASP SER ARG ALA ARG GLN LEU ASN ALA ALA SEQRES 9 A 265 LEU ASP TYR MET ILE ASN ASP ALA SER SER ALA VAL ARG SEQRES 10 A 265 SER ARG ILE ASP SER SER ARG LEU ALA VAL MET GLY HIS SEQRES 11 A 265 SER MET GLY GLY GLY GLY THR LEU ARG LEU ALA SER GLN SEQRES 12 A 265 ARG PRO ASP LEU LYS ALA ALA ILE PRO LEU THR PRO TRP SEQRES 13 A 265 HIS LEU ASN LYS ASN TRP SER SER VAL ARG VAL PRO THR SEQRES 14 A 265 LEU ILE ILE GLY ALA ASP LEU ASP THR ILE ALA PRO VAL SEQRES 15 A 265 LEU THR HIS ALA ARG PRO PHE TYR ASN SER LEU PRO THR SEQRES 16 A 265 SER ILE SER LYS ALA TYR LEU GLU LEU ASP GLY ALA THR SEQRES 17 A 265 HIS PHE ALA PRO ASN ILE PRO ASN LYS ILE ILE GLY LYS SEQRES 18 A 265 TYR SER VAL ALA TRP LEU LYS ARG PHE VAL ASP ASN ASP SEQRES 19 A 265 THR ARG TYR THR GLN PHE LEU CYS PRO GLY PRO ARG ASP SEQRES 20 A 265 GLY LEU PHE GLY GLU VAL GLU GLU TYR ARG SER THR CYS SEQRES 21 A 265 PRO PHE ALA LEU GLU HET CL A 301 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *50(H2 O) HELIX 1 AA1 THR A 12 ALA A 18 1 7 HELIX 2 AA2 THR A 64 SER A 67 5 4 HELIX 3 AA3 VAL A 68 SER A 77 1 10 HELIX 4 AA4 GLN A 93 ASP A 111 1 19 HELIX 5 AA5 SER A 113 SER A 118 1 6 HELIX 6 AA6 SER A 131 ARG A 144 1 14 HELIX 7 AA7 HIS A 185 LEU A 193 1 9 HELIX 8 AA8 PHE A 210 ILE A 214 5 5 HELIX 9 AA9 ASN A 216 ASP A 232 1 17 HELIX 10 AB1 ASP A 234 ARG A 236 5 3 HELIX 11 AB2 TYR A 237 CYS A 242 1 6 SHEET 1 AA1 6 VAL A 25 ALA A 30 0 SHEET 2 AA1 6 GLY A 41 PRO A 46 -1 O ILE A 43 N GLU A 28 SHEET 3 AA1 6 PHE A 80 ILE A 85 -1 O VAL A 82 N TYR A 44 SHEET 4 AA1 6 TYR A 52 SER A 58 1 N VAL A 55 O VAL A 81 SHEET 5 AA1 6 ILE A 120 HIS A 130 1 O HIS A 130 N SER A 58 SHEET 6 AA1 6 ALA A 149 LEU A 153 1 O LEU A 153 N GLY A 129 SHEET 1 AA2 3 THR A 169 ALA A 174 0 SHEET 2 AA2 3 LYS A 199 LEU A 204 1 O LEU A 204 N GLY A 173 SHEET 3 AA2 3 GLU A 255 SER A 258 -1 O GLU A 255 N GLU A 203 SSBOND 1 CYS A 242 CYS A 260 1555 1555 2.04 CISPEP 1 CYS A 242 PRO A 243 0 0.74 CISPEP 2 CYS A 260 PRO A 261 0 10.78 SITE 1 AC1 1 ARG A 29 CRYST1 36.670 43.150 152.350 90.00 90.00 90.00 P 2 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 0.027270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006564 0.00000