HEADER HYDROLASE 02-OCT-14 4V1S TITLE STRUCTURE OF THE GH76 ALPHA-MANNANASE BT2949 FROM TITLE 2 BACTEROIDES THETAIOTAOMICRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-1,6-MANNANASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.1.101; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: VPI-5482; SOURCE 5 ATCC: 29148; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS HYDROLASE, GLYCOSIDE HYDROLASE, GH76, CAZY, POLYSACCHARIDE KEYWDS 2 UTILISATION, ENZYME-CARBOHYDRATE INTERACTION EXPDTA X-RAY DIFFRACTION AUTHOR A.J.THOMPSON,F.CUSKIN,R.J.SPEARS,J.DABIN,J.P.TURKENBURG,H.J.GILBERT, AUTHOR 2 G.J.DAVIES REVDAT 2 25-FEB-15 4V1S 1 JRNL REVDAT 1 11-FEB-15 4V1S 0 JRNL AUTH A.J.THOMPSON,F.CUSKIN,R.J.SPEARS,J.DABIN,J.P.TURKENBURG, JRNL AUTH 2 H.J.GILBERT,G.J.DAVIES JRNL TITL STRUCTURE OF THE GH76 ALPHA-MANNANASE HOMOLOG, BT2949, JRNL TITL 2 FROM THE GUT SYMBIONT BACTEROIDES THETAIOTAOMICRON JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 408 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25664752 JRNL DOI 10.1107/S1399004714026443 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.12 REMARK 3 NUMBER OF REFLECTIONS : 170173 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 + TEST SET) : 0.15039 REMARK 3 R VALUE (WORKING SET) : 0.14879 REMARK 3 FREE R VALUE : 0.18040 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 9002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.500 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.539 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7298 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.254 REMARK 3 BIN FREE R VALUE SET COUNT : 391 REMARK 3 BIN FREE R VALUE : 0.314 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5732 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 1116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.300 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.61 REMARK 3 B22 (A**2) : 1.76 REMARK 3 B33 (A**2) : -0.15 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.513 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6053 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5435 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8256 ; 1.350 ; 1.927 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12502 ; 0.988 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 758 ; 5.336 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 290 ;35.954 ;24.552 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 965 ;12.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;18.871 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 882 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6981 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1506 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2637 ; 0.266 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5395 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3063 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2486 ; 0.078 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 199 ; 0.113 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.016 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.289 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.195 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.235 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2914 ; 3.022 ; 1.702 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2913 ; 3.019 ; 1.700 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3650 ; 3.534 ; 2.559 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3139 ; 3.129 ; 1.878 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4584 ;0.3779 ; 2.736 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11488 ; 2.769 ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): 364 ;53.911 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 12087 ;14.199 ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4V1S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-14. REMARK 100 THE PDBE ID CODE IS EBI-60682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 179372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.50 REMARK 200 RESOLUTION RANGE LOW (A) : 46.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.7 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 6.7 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.3 REMARK 200 R MERGE FOR SHELL (I) : 0.68 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.80 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: PREVIOUSLY SOLVED SELENOMETHIONINE REMARK 200 DERIVATIVE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 7.0, 1.25 M AMMONIUM REMARK 280 PHOSPHATE 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 60.51500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.80200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.51500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.80200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 ILE A 2 REMARK 465 ARG A 3 REMARK 465 ILE A 4 REMARK 465 SER A 5 REMARK 465 ASN A 6 REMARK 465 LYS A 7 REMARK 465 ILE A 8 REMARK 465 LYS A 9 REMARK 465 THR A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 ALA A 13 REMARK 465 MET A 14 REMARK 465 LEU A 15 REMARK 465 SER A 16 REMARK 465 PHE A 17 REMARK 465 VAL A 18 REMARK 465 GLN A 19 REMARK 465 VAL A 20 REMARK 465 THR A 21 REMARK 465 SER A 22 REMARK 465 GLY A 23 REMARK 465 CYS A 24 REMARK 465 ASP A 25 REMARK 465 ALA A 26 REMARK 465 THR A 27 REMARK 465 VAL A 28 REMARK 465 GLN A 29 REMARK 465 ASP A 30 REMARK 465 ILE A 31 REMARK 465 ILE A 32 REMARK 465 ILE A 33 REMARK 465 ASP A 34 REMARK 465 THR A 35 REMARK 465 ASP A 36 REMARK 465 ASP A 396 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 ARG B 3 REMARK 465 ILE B 4 REMARK 465 SER B 5 REMARK 465 ASN B 6 REMARK 465 LYS B 7 REMARK 465 ILE B 8 REMARK 465 LYS B 9 REMARK 465 THR B 10 REMARK 465 LEU B 11 REMARK 465 LEU B 12 REMARK 465 ALA B 13 REMARK 465 MET B 14 REMARK 465 LEU B 15 REMARK 465 SER B 16 REMARK 465 PHE B 17 REMARK 465 VAL B 18 REMARK 465 GLN B 19 REMARK 465 VAL B 20 REMARK 465 THR B 21 REMARK 465 SER B 22 REMARK 465 GLY B 23 REMARK 465 CYS B 24 REMARK 465 ASP B 25 REMARK 465 ALA B 26 REMARK 465 THR B 27 REMARK 465 VAL B 28 REMARK 465 GLN B 29 REMARK 465 ASP B 30 REMARK 465 ILE B 31 REMARK 465 ILE B 32 REMARK 465 ILE B 33 REMARK 465 ASP B 34 REMARK 465 THR B 35 REMARK 465 ASP B 36 REMARK 465 ASP B 396 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 37 CG CD REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 ILE A 41 CG1 CG2 CD1 REMARK 470 ASN A 43 CG OD1 ND2 REMARK 470 GLN A 77 CG CD OE1 NE2 REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 223 CG CD OE1 NE2 REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 GLU A 370 CG CD OE1 OE2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 ASN A 395 CG OD1 ND2 REMARK 470 VAL B 39 CG1 CG2 REMARK 470 GLU B 40 CG CD OE1 OE2 REMARK 470 ASN B 43 CG OD1 ND2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 LYS B 136 CG CD CE NZ REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 242 CG CD CE NZ REMARK 470 LYS B 282 CG CD CE NZ REMARK 470 GLU B 370 CG CD OE1 OE2 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 O1 GOL A 401 O HOH A 963 2.19 REMARK 500 O A HOH A 1014 O HOH A 1034 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 O1 GOL B 402 O HOH A 638 4444 2.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 375 CG - CD - NE ANGL. DEV. = -20.7 DEGREES REMARK 500 ARG A 375 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES 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 120 99.40 -175.55 REMARK 500 VAL A 194 -81.13 -124.06 REMARK 500 ASN B 120 102.24 -176.78 REMARK 500 VAL B 194 -80.90 -123.84 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 GOL A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V1R RELATED DB: PDB REMARK 900 STRUCTURE OF A SELENOMETHIONINE DERIVATIVE OF THE GH76 REMARK 900 ALPHA-MANNANASE BT2949 BACTEROIDES THETAIOTAOMICRON REMARK 900 RELATED ID: 4V27 RELATED DB: PDB REMARK 900 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM REMARK 900 BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA- REMARK 900 1,3-ISOFAGOMINE REMARK 900 RELATED ID: 4V28 RELATED DB: PDB REMARK 900 STRUCTURE OF AN E333Q VARIANT OF THE GH99 ENDO-ALPHA REMARK 900 -MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH REMARK 900 MAN-MAN-METHYLUMBELLIFERONE DBREF 4V1S A 1 396 UNP Q8A3K5 Q8A3K5_BACTN 1 396 DBREF 4V1S B 1 396 UNP Q8A3K5 Q8A3K5_BACTN 1 396 SEQRES 1 A 396 MET ILE ARG ILE SER ASN LYS ILE LYS THR LEU LEU ALA SEQRES 2 A 396 MET LEU SER PHE VAL GLN VAL THR SER GLY CYS ASP ALA SEQRES 3 A 396 THR VAL GLN ASP ILE ILE ILE ASP THR ASP PRO GLY VAL SEQRES 4 A 396 GLU ILE GLY ASN ASN ASP TYR TYR THR TRP CYS LYS GLU SEQRES 5 A 396 THR LEU SER VAL ILE ASP LYS ASP LEU LYS ILE SER GLY SEQRES 6 A 396 THR HIS SER TYR TYR GLU ASN GLN ASP ARG SER GLN VAL SEQRES 7 A 396 SER PHE ILE TRP GLY ASN ILE PHE LEU LEU TYR THR TYR SEQRES 8 A 396 THR GLU GLY ILE SER LEU SER LYS SER GLU TRP SER ASP SEQRES 9 A 396 ALA LEU MET ASN CYS PHE LEU ASN PHE ASP ASN TYR TRP SEQRES 10 A 396 HIS PRO ASN TYR LYS GLY ILE ALA GLY TYR ALA THR LEU SEQRES 11 A 396 PRO THR SER ALA GLU LYS VAL PRO ASP ARG PHE TYR ASP SEQRES 12 A 396 GLU ASN GLY TRP THR ALA ILE GLY LEU CYS ASP ALA TYR SEQRES 13 A 396 LEU ALA THR GLN ASN ASN SER TYR LEU GLU LYS ALA LYS SEQRES 14 A 396 GLY ALA LEU ALA PHE SER LEU SER GLY GLU ASP ASN VAL SEQRES 15 A 396 LEU GLY GLY GLY ILE TYR PHE GLN GLU THR PHE VAL SER SEQRES 16 A 396 LEU PRO VAL GLN LYS ASN THR ILE CYS SER ALA VAL THR SEQRES 17 A 396 MET LEU SER CYS MET LYS LEU TYR GLU ILE THR GLN ASP SEQRES 18 A 396 ARG GLN TYR LEU ASP ALA ALA ILE ARG ILE ASN ASP TRP SEQRES 19 A 396 THR VAL GLU ASN LEU LEU ASP LYS SER ASP ASN LEU LEU SEQRES 20 A 396 TRP ASP ALA LYS MET VAL ALA ASP GLY SER VAL ASN THR SEQRES 21 A 396 GLN LYS TRP SER TYR ASN ALA GLY PHE MET ILE ARG SER SEQRES 22 A 396 TRP LEU LYS MET TYR GLN ALA THR LYS ASP GLU LYS TYR SEQRES 23 A 396 LEU SER GLN ALA LYS ALA THR LEU ALA SER SER GLU ALA SEQRES 24 A 396 LYS TRP TYR ASN SER ILE ASN GLY ALA LEU ASN ASP PRO SEQRES 25 A 396 GLY TYR PHE ALA PHE SER ILE ILE ASP SER TRP PHE ASP SEQRES 26 A 396 MET TYR ASP THR ASP LYS ASN THR VAL TRP LEU THR LYS SEQRES 27 A 396 ALA PHE HIS ALA ILE ASN PHE ILE HIS ASN LYS LEU ARG SEQRES 28 A 396 ASP GLY ASN GLY ARG TYR PRO GLU HIS TRP GLY THR PRO SEQRES 29 A 396 THR THR SER ASN LEU GLU LYS TYR ASP LEU ARG PHE SER SEQRES 30 A 396 THR VAL ALA ALA TYR MET TYR MET ARG ALA ALA ASN TYR SEQRES 31 A 396 LYS ARG ILE LEU ASN ASP SEQRES 1 B 396 MET ILE ARG ILE SER ASN LYS ILE LYS THR LEU LEU ALA SEQRES 2 B 396 MET LEU SER PHE VAL GLN VAL THR SER GLY CYS ASP ALA SEQRES 3 B 396 THR VAL GLN ASP ILE ILE ILE ASP THR ASP PRO GLY VAL SEQRES 4 B 396 GLU ILE GLY ASN ASN ASP TYR TYR THR TRP CYS LYS GLU SEQRES 5 B 396 THR LEU SER VAL ILE ASP LYS ASP LEU LYS ILE SER GLY SEQRES 6 B 396 THR HIS SER TYR TYR GLU ASN GLN ASP ARG SER GLN VAL SEQRES 7 B 396 SER PHE ILE TRP GLY ASN ILE PHE LEU LEU TYR THR TYR SEQRES 8 B 396 THR GLU GLY ILE SER LEU SER LYS SER GLU TRP SER ASP SEQRES 9 B 396 ALA LEU MET ASN CYS PHE LEU ASN PHE ASP ASN TYR TRP SEQRES 10 B 396 HIS PRO ASN TYR LYS GLY ILE ALA GLY TYR ALA THR LEU SEQRES 11 B 396 PRO THR SER ALA GLU LYS VAL PRO ASP ARG PHE TYR ASP SEQRES 12 B 396 GLU ASN GLY TRP THR ALA ILE GLY LEU CYS ASP ALA TYR SEQRES 13 B 396 LEU ALA THR GLN ASN ASN SER TYR LEU GLU LYS ALA LYS SEQRES 14 B 396 GLY ALA LEU ALA PHE SER LEU SER GLY GLU ASP ASN VAL SEQRES 15 B 396 LEU GLY GLY GLY ILE TYR PHE GLN GLU THR PHE VAL SER SEQRES 16 B 396 LEU PRO VAL GLN LYS ASN THR ILE CYS SER ALA VAL THR SEQRES 17 B 396 MET LEU SER CYS MET LYS LEU TYR GLU ILE THR GLN ASP SEQRES 18 B 396 ARG GLN TYR LEU ASP ALA ALA ILE ARG ILE ASN ASP TRP SEQRES 19 B 396 THR VAL GLU ASN LEU LEU ASP LYS SER ASP ASN LEU LEU SEQRES 20 B 396 TRP ASP ALA LYS MET VAL ALA ASP GLY SER VAL ASN THR SEQRES 21 B 396 GLN LYS TRP SER TYR ASN ALA GLY PHE MET ILE ARG SER SEQRES 22 B 396 TRP LEU LYS MET TYR GLN ALA THR LYS ASP GLU LYS TYR SEQRES 23 B 396 LEU SER GLN ALA LYS ALA THR LEU ALA SER SER GLU ALA SEQRES 24 B 396 LYS TRP TYR ASN SER ILE ASN GLY ALA LEU ASN ASP PRO SEQRES 25 B 396 GLY TYR PHE ALA PHE SER ILE ILE ASP SER TRP PHE ASP SEQRES 26 B 396 MET TYR ASP THR ASP LYS ASN THR VAL TRP LEU THR LYS SEQRES 27 B 396 ALA PHE HIS ALA ILE ASN PHE ILE HIS ASN LYS LEU ARG SEQRES 28 B 396 ASP GLY ASN GLY ARG TYR PRO GLU HIS TRP GLY THR PRO SEQRES 29 B 396 THR THR SER ASN LEU GLU LYS TYR ASP LEU ARG PHE SER SEQRES 30 B 396 THR VAL ALA ALA TYR MET TYR MET ARG ALA ALA ASN TYR SEQRES 31 B 396 LYS ARG ILE LEU ASN ASP HET GOL A 400 12 HET GOL A 401 6 HET GOL B 400 6 HET GOL B 401 6 HET GOL B 402 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 5(C3 H8 O3) FORMUL 4 HOH *1116(H2 O) HELIX 1 1 PRO A 37 GLY A 42 1 6 HELIX 2 2 ASP A 45 LYS A 62 1 18 HELIX 3 3 PHE A 80 SER A 98 1 19 HELIX 4 4 SER A 98 ASN A 115 1 18 HELIX 5 5 PHE A 141 GLN A 160 1 20 HELIX 6 6 ASN A 161 GLY A 178 1 18 HELIX 7 7 ASN A 181 GLY A 185 5 5 HELIX 8 8 THR A 202 GLN A 220 1 19 HELIX 9 9 ASP A 221 LEU A 240 1 20 HELIX 10 10 TRP A 263 LYS A 282 1 20 HELIX 11 11 ASP A 283 TYR A 302 1 20 HELIX 12 12 PRO A 312 LYS A 331 1 20 HELIX 13 13 THR A 333 LEU A 350 1 18 HELIX 14 14 ASP A 373 ASN A 395 1 23 HELIX 15 15 PRO B 37 GLY B 42 1 6 HELIX 16 16 ASP B 45 LYS B 62 1 18 HELIX 17 17 PHE B 80 SER B 98 1 19 HELIX 18 18 SER B 98 ASN B 115 1 18 HELIX 19 19 PHE B 141 GLN B 160 1 20 HELIX 20 20 ASN B 161 GLY B 178 1 18 HELIX 21 21 ASN B 181 GLY B 185 5 5 HELIX 22 22 THR B 202 GLN B 220 1 19 HELIX 23 23 ASP B 221 LEU B 240 1 20 HELIX 24 24 TRP B 263 LYS B 282 1 20 HELIX 25 25 ASP B 283 TYR B 302 1 20 HELIX 26 26 PRO B 312 LYS B 331 1 20 HELIX 27 27 THR B 333 LEU B 350 1 18 HELIX 28 28 ASP B 373 ASN B 395 1 23 SHEET 1 AA 2 TRP A 117 TYR A 121 0 SHEET 2 AA 2 ILE A 124 TYR A 127 -1 O ILE A 124 N TYR A 121 SHEET 1 AB 3 GLN A 199 ASN A 201 0 SHEET 2 AB 3 ALA A 250 MET A 252 -1 O LYS A 251 N LYS A 200 SHEET 3 AB 3 VAL A 258 ASN A 259 -1 N ASN A 259 O ALA A 250 SHEET 1 BA 2 TRP B 117 TYR B 121 0 SHEET 2 BA 2 ILE B 124 TYR B 127 -1 O ILE B 124 N TYR B 121 SHEET 1 BB 3 GLN B 199 ASN B 201 0 SHEET 2 BB 3 ALA B 250 MET B 252 -1 O LYS B 251 N LYS B 200 SHEET 3 BB 3 VAL B 258 ASN B 259 -1 N ASN B 259 O ALA B 250 SITE 1 AC1 6 PHE A 189 ASN A 201 ASP A 249 TRP A 263 SITE 2 AC1 6 TYR A 265 HOH A 517 SITE 1 AC2 8 TRP A 82 ASP A 143 TRP A 147 ILE A 203 SITE 2 AC2 8 TYR A 265 PHE A 315 HOH A 721 HOH A 963 SITE 1 AC3 6 ASN B 201 ILE B 203 ASP B 249 TRP B 263 SITE 2 AC3 6 TYR B 265 HOH B 509 SITE 1 AC4 7 TRP B 82 ASP B 143 GLU B 144 TRP B 147 SITE 2 AC4 7 ILE B 203 TYR B 265 HOH B 780 SITE 1 AC5 8 SER A 243 ASP A 244 ASN A 245 SER A 296 SITE 2 AC5 8 HOH A 569 HOH A 583 HOH A 638 LYS B 59 CRYST1 81.677 121.030 125.604 90.00 90.00 90.00 P 2 21 21 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 0.012243 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007962 0.00000 MTRIX1 1 -1.000000 0.001049 0.000192 -40.79000 1 MTRIX2 1 0.001050 1.000000 0.007581 0.05268 1 MTRIX3 1 -0.000184 0.007581 -1.000000 -8.27900 1