HEADER HYDROLASE 07-OCT-16 5M17 TITLE STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES TITLE 2 XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-1,2-DIDEOXYMANNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYL HYDROLASE FAMILY 71; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES XYLANISOLVENS XB1A; SOURCE 3 ORGANISM_TAXID: 657309; SOURCE 4 GENE: BXY_34140; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENDOMANNANASE, ENDOMANNOSIDASE, GH99, N-GLYCOSYLATION, GLYCOSYLATION, KEYWDS 2 INHIBITOR, INHIBITION, SHAPE, CHARGE, MANNOBIOSE, MANNOSE, KEYWDS 3 GLYCOBIOLOGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PETRICEVIC,L.F.SOBALA,P.Z.FERNANDES,L.RAICH,A.J.THOMPSON, AUTHOR 2 G.BERNARDO-SEISDEDOS,O.MILLET,S.ZHU,M.SOLLOGOUB,C.ROVIRA,J.JIMENEZ- AUTHOR 3 BARBERO,G.J.DAVIES,S.J.WILLIAMS REVDAT 6 17-JAN-24 5M17 1 REMARK REVDAT 5 10-FEB-21 5M17 1 HETSYN REVDAT 4 29-JUL-20 5M17 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 08-FEB-17 5M17 1 JRNL REVDAT 2 25-JAN-17 5M17 1 JRNL REVDAT 1 11-JAN-17 5M17 0 JRNL AUTH M.PETRICEVIC,L.F.SOBALA,P.Z.FERNANDES,L.RAICH,A.J.THOMPSON, JRNL AUTH 2 G.BERNARDO-SEISDEDOS,O.MILLET,S.ZHU,M.SOLLOGOUB, JRNL AUTH 3 J.JIMENEZ-BARBERO,C.ROVIRA,G.J.DAVIES,S.J.WILLIAMS JRNL TITL CONTRIBUTION OF SHAPE AND CHARGE TO THE INHIBITION OF A JRNL TITL 2 FAMILY GH99 ENDO-ALPHA-1,2-MANNANASE. JRNL REF J. AM. CHEM. SOC. V. 139 1089 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 27992199 JRNL DOI 10.1021/JACS.6B10075 REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 179143 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) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 9325 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) : 1.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10265 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 517 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.20000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.020 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.013 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.563 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.983 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3405 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3097 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4731 ; 1.530 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7211 ; 1.072 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 8.554 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;34.835 ;23.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 551 ;12.082 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.911 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 496 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4005 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 862 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1574 ; 0.976 ; 1.371 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1572 ; 0.974 ; 1.369 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2000 ; 1.338 ; 2.071 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2001 ; 1.338 ; 2.072 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1831 ; 1.416 ; 1.527 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1831 ; 1.416 ; 1.527 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2676 ; 1.742 ; 2.230 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4054 ; 3.074 ;17.026 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3973 ; 2.722 ;16.345 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6502 ; 1.608 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 277 ;28.921 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6487 ; 7.813 ; 5.000 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 : NULL 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 REMARK 4 REMARK 4 5M17 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 1.0-0-G66AC5D4 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 188472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 76.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.98900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.8.0135 REMARK 200 STARTING MODEL: 4UTF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 M SODIUM ACETATE, PH 7.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 54.28800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.28800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.87300 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 54.28800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.28800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.87300 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 54.28800 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 54.28800 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.87300 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 54.28800 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 54.28800 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.87300 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: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 KCAL/MOL 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 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 HOH A 708 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 -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 PRO A 11 REMARK 465 ARG A 12 REMARK 465 GLY A 13 REMARK 465 SER A 14 REMARK 465 HIS A 15 REMARK 465 MET A 16 REMARK 465 ASP A 17 REMARK 465 ASP A 18 REMARK 465 ASN A 19 REMARK 465 ASN A 20 REMARK 465 PRO A 21 REMARK 465 SER A 22 REMARK 465 ASN A 23 REMARK 465 SER A 24 REMARK 465 GLU A 25 REMARK 465 ASN A 26 REMARK 465 ASN A 27 REMARK 465 GLY A 28 REMARK 465 GLY A 29 REMARK 465 ASN A 30 REMARK 465 GLN A 380 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 ASN A 31 CG OD1 ND2 REMARK 470 GLU A 52 CD OE1 OE2 REMARK 470 ASN A 76 OD1 ND2 REMARK 470 LYS A 108 NZ REMARK 470 ASP A 130 OD1 OD2 REMARK 470 LYS A 135 NZ REMARK 470 LYS A 146 CE NZ REMARK 470 LYS A 147 CE NZ REMARK 470 LYS A 272 CD CE NZ REMARK 470 LYS A 275 CD CE NZ REMARK 470 GLU A 360 CD OE1 OE2 REMARK 470 LYS A 374 CE NZ 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 HIS A 60 -35.08 68.81 REMARK 500 THR A 231 -73.06 -101.68 REMARK 500 SER A 232 -150.94 -95.90 REMARK 500 TYR A 252 -60.26 61.01 REMARK 500 ASN A 332 43.27 -152.73 REMARK 500 GLU A 357 -122.23 56.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 357 ASN A 358 43.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 357 11.84 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 909 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 910 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A 911 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A 912 DISTANCE = 8.15 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AD1 RELATED DB: PDB REMARK 900 4AD1 CONTAINS THE SAME PROTEIN (APO). REMARK 900 RELATED ID: 4AD2 RELATED DB: PDB REMARK 900 4AD2 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- REMARK 900 ISOFAGOMINE. REMARK 900 RELATED ID: 4AD3 RELATED DB: PDB REMARK 900 4AD3 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- REMARK 900 DEOXYMANNOJIRIMYCIN. REMARK 900 RELATED ID: 4AD4 RELATED DB: PDB REMARK 900 4AD4 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- REMARK 900 ISOFAGOMINE AND ALPHA-1,2- MANNOBIOSE. REMARK 900 RELATED ID: 4AD5 RELATED DB: PDB REMARK 900 4AD5 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- REMARK 900 DEOXYMANNOJIRIMYCIN AND ALPHA-1,2-MANNOBIOSE. REMARK 900 RELATED ID: 4UTF RELATED DB: PDB REMARK 900 4UTF CONTAINS THE SAME PROTEIN IN COMPLEX WITH MANNOSE-ALPHA-1,3- REMARK 900 ISOFAGOMINE AND ALPHA- 1,2-MANNOBIOSE. REMARK 900 RELATED ID: 4V27 RELATED DB: PDB REMARK 900 4V27 CONTAINS THE SAME PROTEIN IN COMPLEX WITH MANNOSE-ALPHA-1,3- REMARK 900 ISOFAGOMINE. REMARK 900 RELATED ID: 4V28 RELATED DB: PDB REMARK 900 4V28 CONTAINS AN E333Q VARIANT OF THE SAME PROTEIN WITH IN COMPLEX REMARK 900 IN COMPLEX WITH MAN-MAN-METHYLUMBELLIFERONE. DBREF 5M17 A 17 380 UNP D6D1V7 D6D1V7_9BACE 17 380 SEQADV 5M17 MET A -4 UNP D6D1V7 INITIATING METHIONINE SEQADV 5M17 GLY A -3 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 SER A -2 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 SER A -1 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 0 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 1 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 2 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 3 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 4 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 5 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 SER A 6 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 SER A 7 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 GLY A 8 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 LEU A 9 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 VAL A 10 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 PRO A 11 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 ARG A 12 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 GLY A 13 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 SER A 14 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 HIS A 15 UNP D6D1V7 EXPRESSION TAG SEQADV 5M17 MET A 16 UNP D6D1V7 EXPRESSION TAG SEQRES 1 A 385 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 385 LEU VAL PRO ARG GLY SER HIS MET ASP ASP ASN ASN PRO SEQRES 3 A 385 SER ASN SER GLU ASN ASN GLY GLY ASN ASN ASN LEU GLY SEQRES 4 A 385 THR GLU LEU ASP TYR ASP THR PHE CYS PHE TYR TYR ASP SEQRES 5 A 385 TRP TYR GLY SER GLU ALA ILE ASP GLY GLN TYR ARG HIS SEQRES 6 A 385 TRP ALA HIS ALA ILE ALA PRO ASP PRO ASN GLY GLY SER SEQRES 7 A 385 GLY GLN ASN PRO GLY THR ILE PRO GLY THR GLN GLU SER SEQRES 8 A 385 ILE ALA SER ASN PHE TYR PRO GLN LEU GLY ARG TYR SER SEQRES 9 A 385 SER SER ASP PRO ASN ILE LEU THR LYS HIS MET ASP MET SEQRES 10 A 385 PHE VAL MET ALA ARG THR GLY VAL LEU ALA LEU THR TRP SEQRES 11 A 385 TRP ASN GLU GLN ASP GLU THR GLU ALA LYS ARG ILE GLY SEQRES 12 A 385 LEU ILE LEU ASP ALA ALA ASP LYS LYS LYS ILE LYS VAL SEQRES 13 A 385 CYS PHE HIS LEU GLU PRO TYR PRO SER ARG ASN VAL GLN SEQRES 14 A 385 ASN LEU ARG GLU ASN ILE VAL LYS LEU ILE THR ARG TYR SEQRES 15 A 385 GLY ASN HIS PRO ALA PHE TYR ARG LYS ASP GLY LYS PRO SEQRES 16 A 385 LEU PHE PHE ILE TYR ASP SER TYR LEU ILE GLU PRO SER SEQRES 17 A 385 GLU TRP GLU LYS LEU LEU SER PRO GLY GLY SER ILE THR SEQRES 18 A 385 ILE ARG ASN THR ALA TYR ASP ALA LEU MET ILE GLY LEU SEQRES 19 A 385 TRP THR SER SER PRO THR VAL GLN ARG PRO PHE ILE LEU SEQRES 20 A 385 ASN ALA HIS PHE ASP GLY PHE TYR THR TYR PHE ALA ALA SEQRES 21 A 385 THR GLY PHE THR TYR GLY SER THR PRO THR ASN TRP VAL SEQRES 22 A 385 SER MET GLN LYS TRP ALA LYS GLU ASN GLY LYS ILE PHE SEQRES 23 A 385 ILE PRO SER VAL GLY PRO GLY TYR ILE ASP THR ARG ILE SEQRES 24 A 385 ARG PRO TRP ASN GLY SER VAL ILE ARG THR ARG THR ASP SEQRES 25 A 385 GLY GLN TYR TYR ASP ALA MET TYR ARG LYS ALA ILE GLU SEQRES 26 A 385 ALA GLY VAL SER ALA ILE SER ILE THR SER PHE ASN GLU SEQRES 27 A 385 TRP HIS GLU GLY SER GLN ILE GLU PRO ALA VAL PRO TYR SEQRES 28 A 385 THR SER SER GLU PHE THR TYR LEU ASP TYR GLU ASN ARG SEQRES 29 A 385 GLU PRO ASP TYR TYR LEU THR ARG THR ALA TYR TRP VAL SEQRES 30 A 385 GLY LYS PHE ARG GLU SER LYS GLN HET 7D1 B 1 10 HET MAN B 2 11 HET EDO A 401 4 HET EDO A 402 4 HET ACT A 403 4 HETNAM 7D1 1,5-ANHYDRO-2-DEOXY-D-ARABINO-HEXITOL HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN 7D1 (2~{R},3~{S},4~{R})-2-(HYDROXYMETHYL)OXANE-3,4-DIOL; 1, HETSYN 2 7D1 2-DIDEOXY-D-MANNOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 7D1 C6 H12 O4 FORMUL 2 MAN C6 H12 O6 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 HOH *412(H2 O) HELIX 1 AA1 SER A 51 GLY A 56 1 6 HELIX 2 AA2 ASP A 102 ARG A 117 1 16 HELIX 3 AA3 ASP A 130 LYS A 147 1 18 HELIX 4 AA4 ASN A 162 GLY A 178 1 17 HELIX 5 AA5 ASP A 196 ILE A 200 5 5 HELIX 6 AA6 GLU A 201 SER A 210 1 10 HELIX 7 AA7 SER A 233 HIS A 245 1 13 HELIX 8 AA8 THR A 263 THR A 265 5 3 HELIX 9 AA9 ASN A 266 ASN A 277 1 12 HELIX 10 AB1 ASN A 298 ILE A 302 5 5 HELIX 11 AB2 ARG A 305 ASP A 307 5 3 HELIX 12 AB3 GLY A 308 ALA A 321 1 14 HELIX 13 AB4 GLU A 333 GLY A 337 5 5 HELIX 14 AB5 ASP A 362 LYS A 379 1 18 SHEET 1 AA1 9 ILE A 280 ILE A 282 0 SHEET 2 AA1 9 GLY A 248 TYR A 250 1 N PHE A 249 O ILE A 282 SHEET 3 AA1 9 LEU A 225 LEU A 229 1 N GLY A 228 O GLY A 248 SHEET 4 AA1 9 LEU A 191 ILE A 194 1 N PHE A 192 O ILE A 227 SHEET 5 AA1 9 LYS A 150 LEU A 155 1 N LEU A 155 O PHE A 193 SHEET 6 AA1 9 THR A 118 TRP A 125 1 N LEU A 121 O LYS A 150 SHEET 7 AA1 9 ASP A 38 TYR A 45 1 N CYS A 43 O VAL A 120 SHEET 8 AA1 9 ILE A 326 ILE A 328 1 O ILE A 328 N PHE A 42 SHEET 9 AA1 9 SER A 284 VAL A 285 1 N VAL A 285 O SER A 327 SHEET 1 AA2 2 ALA A 62 ALA A 64 0 SHEET 2 AA2 2 THR A 79 PRO A 81 -1 O ILE A 80 N HIS A 63 LINK O3 7D1 B 1 C1 MAN B 2 1555 1555 1.42 CISPEP 1 THR A 329 SER A 330 0 11.58 CRYST1 108.576 108.576 67.746 90.00 90.00 90.00 I 4 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 0.009210 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014761 0.00000