HEADER HYDROLASE 14-JUN-19 6K98 TITLE SUBSTRATES PROMISCUITY OF XYLOGLUCANASES AND ENDOGLUCANASES OF TITLE 2 GLYCOSIDE HYDROLASE 12 FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GH12 BETA-1, 4-ENDOGLUCANASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLYCOSIDE HYDROLASE FAMILY 12 ENDOGLUCANASE; COMPND 5 EC: 3.2.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS FISCHERI; SOURCE 3 ORGANISM_TAXID: 36630; SOURCE 4 VARIANT: CGMCC 3.15369; SOURCE 5 GENE: NFEG12A; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PHAFFII CBS 7435; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 981350 KEYWDS ENDOGLUCANASE, GLYCOSIDE HYDROLASE FAMILY 12, PROTEIN FIBRIL, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HONG,T.TAO,S.PENGJUN,C.JIAMING,W.XIAOYU,H.CHEN,B.YINGGUO,Y.BIN REVDAT 2 22-NOV-23 6K98 1 REMARK REVDAT 1 17-JUN-20 6K98 0 JRNL AUTH Y.HONG,T.TAO,S.PENGJUN,C.JIAMING,W.XIAOYU,H.CHEN,B.YINGGUO, JRNL AUTH 2 Y.BIN JRNL TITL SUBSTRATES PROMISCUITY OF XYLOGLUCANASES AND ENDOGLUCANASES JRNL TITL 2 OF GLYCOSIDE HYDROLASE 12 FAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 29949 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1491 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 57.5449 - 4.5195 1.00 3198 151 0.1423 0.1686 REMARK 3 2 4.5195 - 3.5874 0.96 2920 143 0.1442 0.1608 REMARK 3 3 3.5874 - 3.1340 1.00 2978 159 0.1921 0.2117 REMARK 3 4 3.1340 - 2.8474 1.00 2944 167 0.2237 0.2515 REMARK 3 5 2.8474 - 2.6434 1.00 2959 143 0.2446 0.2843 REMARK 3 6 2.6434 - 2.4875 1.00 2912 173 0.2508 0.2984 REMARK 3 7 2.4875 - 2.3629 1.00 2923 159 0.2764 0.2781 REMARK 3 8 2.3629 - 2.2601 0.99 2878 149 0.2786 0.3319 REMARK 3 9 2.2601 - 2.1731 0.69 2056 94 0.3035 0.2908 REMARK 3 10 2.1731 - 2.0981 0.71 2052 119 0.3026 0.3532 REMARK 3 11 2.0981 - 2.0325 0.22 638 34 0.3080 0.3087 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.740 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 : 0.007 1800 REMARK 3 ANGLE : 0.839 2470 REMARK 3 CHIRALITY : 0.055 264 REMARK 3 PLANARITY : 0.005 316 REMARK 3 DIHEDRAL : 5.876 1351 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 6K98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00919 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29949 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.032 REMARK 200 RESOLUTION RANGE LOW (A) : 57.522 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.52 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 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: PHASER REMARK 200 STARTING MODEL: 1KS4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NFEG12A WAS CONCENTRATED TO 10 MG/ML REMARK 280 IN A BUFFER CONTAINING 100 MM CITRIC ACID-NA2HPO4 (PH 7.2). THE REMARK 280 PROTEIN WAS CRYSTALLIZED IN A MOTHER LIQUID WITH 0.1 M CITRATE REMARK 280 (PH 5.0) AND 16% (W/V) PEG 20000 USING THE HANGING DROP VAPOR REMARK 280 DIFFUSION METHOD IN 24-WELL PLATES. NFEG12A CRYSTALS WAS REMARK 280 TRANSFERRED TO A RESERVOIR SOLUTION SUPPLEMENTED WITH 25% (V/V) REMARK 280 ETHYLENE GLYCOL TO GROWN. OBTAINED CRYSTALS WERE CRYOPROTECTED REMARK 280 WITH 25% (V/V) 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE REMARK 280 MOUNTED ON A NYLON LOOP AND COOLED IMMEDIATELY IN LIQUID REMARK 280 NITROGEN PRIOR TO DATA COLLECTION., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 59.96400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.35400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.35400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.94600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.35400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.35400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.98200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.35400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.35400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.94600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.35400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.35400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.98200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.96400 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: 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 NH2 ARG A 14 O ALA A 216 2.19 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 GLN A 1 -145.12 -160.44 REMARK 500 SER A 126 59.13 -90.85 REMARK 500 SER A 151 -95.26 -107.18 REMARK 500 PHE A 202 -68.85 -104.31 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6K98 A 0 219 UNP A0A1L6CE30_9EURO DBREF2 6K98 A A0A1L6CE30 16 234 SEQRES 1 A 219 ALA GLN THR LEU CYS ASP GLN TYR ALA THR TYR SER ASN SEQRES 2 A 219 GLY ARG TYR THR VAL ASN ASN ASN LEU TRP GLY LYS SER SEQRES 3 A 219 SER GLY SER GLY SER GLN CYS THR TYR VAL ASP SER ILE SEQRES 4 A 219 SER ASN SER GLY VAL ALA TRP HIS THR THR TRP THR TRP SEQRES 5 A 219 SER GLY GLY ASP ASN GLN VAL LYS SER TYR ALA ASN SER SEQRES 6 A 219 GLN VAL SER LEU THR LYS LYS LEU VAL SER GLN ILE SER SEQRES 7 A 219 SER ILE PRO THR THR VAL GLN TRP SER TYR ASP ASN THR SEQRES 8 A 219 ASN THR ARG ALA ASP VAL ALA TYR ASP LEU PHE THR ALA SEQRES 9 A 219 ALA ASP ILE ASN HIS VAL THR TYR SER GLY ASP TYR GLU SEQRES 10 A 219 LEU MET ILE TRP LEU ALA ARG TYR GLY SER VAL GLN PRO SEQRES 11 A 219 ILE GLY SER GLN ILE ASP SER VAL ASN ILE GLY GLY HIS SEQRES 12 A 219 THR TRP GLU LEU TRP TYR GLY GLY SER THR GLN LYS THR SEQRES 13 A 219 TYR SER PHE VAL SER ALA THR PRO ILE THR SER PHE SER SEQRES 14 A 219 GLY ASP VAL MET ASP PHE TRP ASP TYR LEU THR SER ARG SEQRES 15 A 219 HIS GLY TYR PRO ALA SER SER GLN TYR LEU ILE ASN MET SEQRES 16 A 219 GLN PHE GLY THR GLU PRO PHE THR GLY GLY PRO ALA THR SEQRES 17 A 219 LEU ARG VAL SER GLN TRP THR ALA SER VAL ASN FORMUL 2 HOH *80(H2 O) HELIX 1 AA1 GLY A 23 GLY A 27 5 5 HELIX 2 AA2 SER A 74 ILE A 76 5 3 HELIX 3 AA3 VAL A 172 HIS A 183 1 12 HELIX 4 AA4 PRO A 186 SER A 189 5 4 SHEET 1 AA1 6 THR A 2 LEU A 3 0 SHEET 2 AA1 6 SER A 28 SER A 39 -1 O THR A 33 N LEU A 3 SHEET 3 AA1 6 GLY A 42 SER A 52 -1 O ALA A 44 N SER A 37 SHEET 4 AA1 6 TYR A 191 ALA A 216 -1 O VAL A 211 N TRP A 45 SHEET 5 AA1 6 PRO A 80 TYR A 87 -1 N SER A 86 O ARG A 210 SHEET 6 AA1 6 SER A 167 ASP A 171 -1 O GLY A 170 N THR A 81 SHEET 1 AA2 5 THR A 2 LEU A 3 0 SHEET 2 AA2 5 SER A 28 SER A 39 -1 O THR A 33 N LEU A 3 SHEET 3 AA2 5 GLY A 42 SER A 52 -1 O ALA A 44 N SER A 37 SHEET 4 AA2 5 TYR A 191 ALA A 216 -1 O VAL A 211 N TRP A 45 SHEET 5 AA2 5 LYS A 71 LEU A 72 -1 N LYS A 71 O LEU A 192 SHEET 1 AA3 9 THR A 9 SER A 11 0 SHEET 2 AA3 9 TYR A 15 ASN A 18 -1 O VAL A 17 N TYR A 10 SHEET 3 AA3 9 ALA A 62 VAL A 66 -1 O ASN A 63 N ASN A 18 SHEET 4 AA3 9 TYR A 191 ALA A 216 -1 O PHE A 197 N SER A 64 SHEET 5 AA3 9 ARG A 93 ALA A 103 -1 N ALA A 103 O TYR A 191 SHEET 6 AA3 9 TYR A 115 TYR A 124 -1 O TYR A 124 N ALA A 94 SHEET 7 AA3 9 LYS A 155 VAL A 160 1 O PHE A 159 N TRP A 120 SHEET 8 AA3 9 HIS A 142 GLY A 149 -1 N GLU A 145 O VAL A 160 SHEET 9 AA3 9 SER A 132 ILE A 139 -1 N VAL A 137 O TRP A 144 SSBOND 1 CYS A 4 CYS A 32 1555 1555 2.05 CISPEP 1 GLY A 205 PRO A 206 0 2.91 CRYST1 92.708 92.708 119.928 90.00 90.00 90.00 P 43 21 2 8 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 0.010787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008338 0.00000