HEADER HYDROLASE 03-OCT-16 5M03 TITLE STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES TITLE 2 XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-NOEUROMYCIN AND 1,2- TITLE 3 ALPHA-MANNOBIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYL HYDROLASE FAMILY 71; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MET -4: INITIATING METHIONINE RESIDUES -3 - 16: COMPND 6 EXPRESSION TAG 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 NOEUROMYCIN HYDROLASE N- KEYWDS 2 GLYCOSYLATION GLYCOSYLATION INHIBITOR INHIBITION SHAPE CHARGE KEYWDS 3 MANNOBIOSE, 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 5M03 1 REMARK REVDAT 5 10-FEB-21 5M03 1 HETSYN LINK REVDAT 4 29-JUL-20 5M03 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 08-FEB-17 5M03 1 JRNL REVDAT 2 25-JAN-17 5M03 1 JRNL REVDAT 1 11-JAN-17 5M03 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. 1.05 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 170072 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) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8872 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) : 1.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11540 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 609 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2813 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 468 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.50000 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): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.762 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.984 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3382 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3045 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4699 ; 1.673 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7091 ; 1.157 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 8.712 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.320 ;23.136 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 535 ;12.123 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.249 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3932 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 851 ; 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): 1555 ; 1.236 ; 1.444 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1552 ; 1.235 ; 1.441 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1971 ; 1.634 ; 2.179 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1972 ; 1.634 ; 2.181 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1827 ; 1.750 ; 1.568 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1827 ; 1.750 ; 1.568 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2678 ; 1.985 ; 2.297 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4102 ; 3.720 ;18.433 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3984 ; 3.183 ;17.403 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6424 ; 2.387 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 299 ;35.197 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6450 ;10.291 ; 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 : 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 REMARK 4 REMARK 4 5M03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-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 : I04 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 178974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 57.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 1.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.700 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: MODIFIED 4UTF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 54.01650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.01650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.72500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 54.01650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.01650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.72500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 54.01650 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 54.01650 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.72500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 54.01650 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 54.01650 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.72500 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: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 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 723 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 ASN A 31 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 GLU A 52 CD OE1 OE2 REMARK 470 ASN A 76 CG 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 272 CD CE NZ REMARK 470 LYS A 275 CD CE NZ REMARK 470 LYS A 317 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: 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 136 NE - CZ - NH1 ANGL. DEV. = -4.2 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 HIS A 60 -35.45 69.99 REMARK 500 HIS A 60 -35.45 69.58 REMARK 500 THR A 231 -74.09 -100.56 REMARK 500 SER A 232 -149.28 -97.09 REMARK 500 TYR A 252 -61.16 62.49 REMARK 500 ASN A 332 44.25 -156.73 REMARK 500 GLU A 357 -117.04 63.96 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 43.43 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 13.63 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 950 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 951 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 952 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 953 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 954 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 955 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 956 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A 957 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A 958 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH A 959 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A 960 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH A 961 DISTANCE = 9.67 ANGSTROMS REMARK 525 HOH A 962 DISTANCE = 10.23 ANGSTROMS REMARK 525 HOH A 963 DISTANCE = 10.32 ANGSTROMS REMARK 525 HOH A 964 DISTANCE = 10.86 ANGSTROMS REMARK 525 HOH A 965 DISTANCE = 12.35 ANGSTROMS REMARK 525 HOH A 966 DISTANCE = 13.35 ANGSTROMS REMARK 525 HOH A 967 DISTANCE = 13.40 ANGSTROMS REMARK 525 HOH A 968 DISTANCE = 13.79 ANGSTROMS REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE METABOLISM REMARK 630 MOLECULE NAME: ALPHA-D-MANNOPYRANOSE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 MAN A 402 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE 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. REMARK 900 RELATED ID: 5LYR RELATED DB: PDB REMARK 900 5LYR CONTAINS THE SAME PROTEIN IN COMPLEX WITH MANNOSE-ALPHA-1,3- REMARK 900 NOEUROMYCIN ONLY. DBREF 5M03 A 17 380 UNP D6D1V7 D6D1V7_9BACE 17 380 SEQADV 5M03 MET A -4 UNP D6D1V7 INITIATING METHIONINE SEQADV 5M03 GLY A -3 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 SER A -2 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 SER A -1 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 0 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 1 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 2 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 3 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 4 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 5 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 SER A 6 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 SER A 7 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 GLY A 8 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 LEU A 9 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 VAL A 10 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 PRO A 11 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 ARG A 12 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 GLY A 13 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 SER A 14 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 HIS A 15 UNP D6D1V7 EXPRESSION TAG SEQADV 5M03 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 MAN B 1 12 HET MAN B 2 22 HET ACT A 401 4 HET MAN A 402 11 HET MNM A 403 11 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ACT ACETATE ION HETNAM MNM (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL- HETNAM 2 MNM PIPERIDINE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN 3(C6 H12 O6) FORMUL 3 ACT C2 H3 O2 1- FORMUL 5 MNM C6 H13 N O4 FORMUL 6 HOH *468(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 ASP A 362 SER A 378 1 17 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 C1 MAN A 402 O4 MNM A 403 1555 1555 1.43 LINK O2 MAN B 1 C1 AMAN B 2 1555 1555 1.44 LINK O2 MAN B 1 C1 BMAN B 2 1555 1555 1.44 CISPEP 1 THR A 329 SER A 330 0 10.28 CRYST1 108.033 108.033 67.450 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 0.009256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014826 0.00000