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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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