HEADER HYDROLASE 21-MAR-13 4BFN TITLE CRYSTAL STRUCTURE OF THE STARCH-BINDING DOMAIN FROM RHIZOPUS ORYZAE TITLE 2 GLUCOAMYLASE IN COMPLEX WITH ISOMALTOTETRAOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOAMYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STARCH BINDING DOMAIN, RESIDUES 26-131; COMPND 5 EC: 3.2.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOPUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 64495; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET23A KEYWDS HYDROLASE, CARBOHYDRATE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.H.CHU,K.M.LI,S.W.LIN,Y.J.SUN REVDAT 4 20-DEC-23 4BFN 1 HETSYN REVDAT 3 29-JUL-20 4BFN 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 28-MAY-14 4BFN 1 JRNL REVDAT 1 23-OCT-13 4BFN 0 JRNL AUTH C.CHU,K.LI,S.LIN,M.D.CHANG,T.JIANG,Y.SUN JRNL TITL CRYSTAL STRUCTURES OF STARCH BINDING DOMAIN FROM RHIZOPUS JRNL TITL 2 ORYZAE GLUCOAMYLASE IN COMPLEX WITH ISOMALTOOLIGOSACCHARIDE: JRNL TITL 3 INSIGHTS INTO POLYSACCHARIDE BINDING MECHANISM OF CBM21 JRNL TITL 4 FAMILY. JRNL REF PROTEINS V. 82 1079 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 24108499 JRNL DOI 10.1002/PROT.24446 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 19977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1023 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 22.7490 - 2.5220 0.96 2966 146 0.1769 0.2119 REMARK 3 2 2.5220 - 2.0022 0.97 2859 155 0.1699 0.1753 REMARK 3 3 2.0022 - 1.7492 0.97 2802 146 0.1598 0.1754 REMARK 3 4 1.7492 - 1.5893 0.96 2744 160 0.1632 0.2007 REMARK 3 5 1.5893 - 1.4754 0.94 2714 139 0.1650 0.1925 REMARK 3 6 1.4754 - 1.3884 0.91 2577 144 0.1799 0.1925 REMARK 3 7 1.3884 - 1.3189 0.80 2292 133 0.1936 0.2425 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 39.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.64870 REMARK 3 B22 (A**2) : 7.65850 REMARK 3 B33 (A**2) : -4.00970 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 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 : 0.005 895 REMARK 3 ANGLE : 1.111 1222 REMARK 3 CHIRALITY : 0.076 140 REMARK 3 PLANARITY : 0.005 147 REMARK 3 DIHEDRAL : 36.761 362 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: ASN101 LIES BEYOND THE REASONABLE RANGE REMARK 3 OF RAMACHANDRAN PLOT DUE TO ITS INTERACTION WITH THE SURROUNDING REMARK 3 RESIDUES. THUS, ASN101 IS LIMITED IN A RIGID CONDITION. REMARK 4 REMARK 4 4BFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1290056167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2V8L REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-CITRATE PH 5.6, 18% PEG4000 REMARK 280 AND 0.2 M NH4-ACETATE 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 12.88400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.19200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.20150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.19200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.88400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.20150 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, B 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 SER A 6 -24.06 -152.12 REMARK 500 SER A 19 -43.09 -137.57 REMARK 500 ASP A 42 -166.29 -75.04 REMARK 500 SER A 59 -60.99 -108.19 REMARK 500 SER A 73 119.12 -164.75 REMARK 500 SER A 99 -9.60 81.67 REMARK 500 ASN A 101 161.26 63.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ALPHA-D-GLUCOSE (GLC): EACH ALPHA-D-GLUCOSE IS CONNECTED BY REMARK 600 ALPHA-1,6 GLYCOSIDIC LINKAGES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BFO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE STARCH-BINDING DOMAIN FROM RHIZOPUS ORYZAE REMARK 900 GLUCOAMYLASE IN COMPLEX WITH ISOMALTOTRIOSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 ILE 53 IS A CLONING VARIANT FROM A LOCAL STRAIN OF REMARK 999 R. ORYZAE. DBREF 4BFN A 1 106 UNP Q2VC81 Q2VC81_RHIOR 26 131 SEQADV 4BFN ILE A 53 UNP Q2VC81 THR 78 SEE REMARK 999 SEQRES 1 A 106 ALA SER ILE PRO SER SER ALA SER VAL GLN LEU ASP SER SEQRES 2 A 106 TYR ASN TYR ASP GLY SER THR PHE SER GLY LYS ILE TYR SEQRES 3 A 106 VAL LYS ASN ILE ALA TYR SER LYS LYS VAL THR VAL VAL SEQRES 4 A 106 TYR ALA ASP GLY SER ASP ASN TRP ASN ASN ASN GLY ASN SEQRES 5 A 106 ILE ILE ALA ALA SER PHE SER GLY PRO ILE SER GLY SER SEQRES 6 A 106 ASN TYR GLU TYR TRP THR PHE SER ALA SER VAL LYS GLY SEQRES 7 A 106 ILE LYS GLU PHE TYR ILE LYS TYR GLU VAL SER GLY LYS SEQRES 8 A 106 THR TYR TYR ASP ASN ASN ASN SER ALA ASN TYR GLN VAL SEQRES 9 A 106 SER THR HET GLC B 1 12 HET GLC B 2 11 HET GLC B 3 11 HET GLC B 4 11 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 4(C6 H12 O6) FORMUL 3 HOH *140(H2 O) HELIX 1 1 TRP A 47 GLY A 51 5 5 SHEET 1 AA 4 VAL A 9 TYR A 16 0 SHEET 2 AA 4 THR A 20 LYS A 28 -1 O SER A 22 N ASN A 15 SHEET 3 AA 4 TYR A 67 SER A 75 -1 O GLU A 68 N VAL A 27 SHEET 4 AA 4 SER A 57 PRO A 61 -1 O SER A 57 N THR A 71 SHEET 1 AB 4 ILE A 53 ALA A 55 0 SHEET 2 AB 4 LYS A 34 ALA A 41 -1 O VAL A 38 N ILE A 54 SHEET 3 AB 4 GLU A 81 VAL A 88 -1 O GLU A 81 N ALA A 41 SHEET 4 AB 4 LYS A 91 ASP A 95 -1 O LYS A 91 N VAL A 88 SHEET 1 AC 4 ILE A 53 ALA A 55 0 SHEET 2 AC 4 LYS A 34 ALA A 41 -1 O VAL A 38 N ILE A 54 SHEET 3 AC 4 GLU A 81 VAL A 88 -1 O GLU A 81 N ALA A 41 SHEET 4 AC 4 TYR A 102 GLN A 103 -1 O TYR A 102 N PHE A 82 SHEET 1 AD 2 LYS A 91 ASP A 95 0 SHEET 2 AD 2 GLU A 81 VAL A 88 -1 O ILE A 84 N ASP A 95 LINK O6 GLC B 1 C1 GLC B 2 1555 1555 1.35 LINK O6 GLC B 2 C1 GLC B 3 1555 1555 1.37 LINK O6 GLC B 3 C1 GLC B 4 1555 1555 1.34 CRYST1 25.768 48.403 70.384 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 0.038808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014208 0.00000