HEADER HYDROLASE 27-APR-06 2GT4 TITLE CRYSTAL STRUCTURE OF THE Y103F MUTANT OF THE GDP-MANNOSE MANNOSYL TITLE 2 HYDROLASE IN COMPLEX WITH GDP-MANNOSE AND MG+2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-MANNOSE MANNOSYL HYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: GDPMH, COLANIC ACID BIOSYNTHESIS PROTEIN WCAH; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YEFC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11B KEYWDS GDP-MANNOSE HYDROLASE GDP-GLUCOSE HYDROLASE NUDIX GDP GDP-FUCOSE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.GABELLI,M.A.BIANCHET,H.F.AZURMENDI,A.S.MILDVAN,L.A.AMZEL REVDAT 7 25-DEC-24 2GT4 1 REMARK LINK REVDAT 6 30-AUG-23 2GT4 1 REMARK REVDAT 5 20-OCT-21 2GT4 1 SEQADV HETSYN REVDAT 4 29-JUL-20 2GT4 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 18-OCT-17 2GT4 1 REMARK REVDAT 2 24-FEB-09 2GT4 1 VERSN REVDAT 1 12-DEC-06 2GT4 0 JRNL AUTH S.B.GABELLI,H.F.AZURMENDI,M.A.BIANCHET,L.M.AMZEL,A.S.MILDVAN JRNL TITL X-RAY, NMR, AND MUTATIONAL STUDIES OF THE CATALYTIC CYCLE OF JRNL TITL 2 THE GDP-MANNOSE MANNOSYL HYDROLASE REACTION. JRNL REF BIOCHEMISTRY V. 45 11290 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16981689 JRNL DOI 10.1021/BI061239G REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 36594 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1883 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2582 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3906 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 142 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : -3.06000 REMARK 3 B33 (A**2) : 2.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4167 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5656 ; 1.223 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 5.917 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;32.544 ;22.877 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 632 ;15.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3195 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1768 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2740 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 307 ; 0.158 ; 0.200 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): 70 ; 0.198 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.112 ; 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): 2450 ; 0.688 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3817 ; 1.172 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1993 ; 1.655 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1839 ; 2.469 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; 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 : BABINET MODEL WITH 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 2GT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000037516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, MADNESS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36595 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1RYA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5MM GDP-MANNOSE 5MM GLUCOSE 5MM GDP REMARK 280 -MANNOSE 5MM GLUCOSE 100 MM TRIS HCL P8.5 20% PEG 4000, 0.2 MG REMARK 280 ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 68.89250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.94650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.89250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.94650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: BIOLOGICAL ASSEMBLY IS A DIMER (A,B) REMARK 300 C FORMS A DIMER WITH ITS SYMMETRY RELATED PARTNER USING THE 2 FOLD 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 BIOMT1 2 -1.000000 0.000000 0.000000 136.36604 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.08777 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 ND2 ASN C 39 C1 BMA C 202 1.29 REMARK 500 ND2 ASN B 39 C1 BMA B 202 1.36 REMARK 500 ND2 ASN B 39 O5 BMA B 202 1.66 REMARK 500 ND2 ASN C 39 O5 BMA C 202 1.91 REMARK 500 N MET A 1 O HOH A 444 1.93 REMARK 500 NH1 ARG C 37 O PRO C 41 1.95 REMARK 500 O4 BMA C 202 O HOH C 413 2.16 REMARK 500 NH2 ARG B 37 O6A GDD B 201 2.18 REMARK 500 O4 BMA B 202 O2B GDD B 201 2.19 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 MET A 2 104.40 -164.59 REMARK 500 ASP A 92 -168.80 -114.21 REMARK 500 ASP B 92 -167.60 -112.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BMA B 202 REMARK 610 BMA C 202 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE2 85.5 REMARK 620 3 GDD A 201 O2B 102.0 169.6 REMARK 620 4 GDD A 201 O2A 98.9 98.3 73.6 REMARK 620 5 HOH A 411 O 165.5 94.2 80.4 95.5 REMARK 620 6 HOH A 455 O 86.5 103.5 84.3 157.9 79.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 50 O REMARK 620 2 GLU B 70 OE2 73.3 REMARK 620 3 GDD B 201 O2B 101.6 170.1 REMARK 620 4 GDD B 201 O2A 98.5 98.2 74.0 REMARK 620 5 HOH B 402 O 85.1 90.0 98.1 171.8 REMARK 620 6 HOH B 417 O 160.9 90.0 96.3 93.0 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY C 50 O REMARK 620 2 GLU C 70 OE2 90.7 REMARK 620 3 GDD C 201 O2B 97.5 165.8 REMARK 620 4 GDD C 201 O2A 101.9 90.0 77.1 REMARK 620 5 BMA C 202 O4 132.2 119.4 62.4 113.3 REMARK 620 6 HOH C 413 O 175.0 93.4 79.1 80.9 42.9 REMARK 620 7 HOH C 425 O 84.9 101.6 90.6 166.5 55.0 91.5 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RYA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN REMARK 900 COMPLEX WITH GDP AND MG REMARK 900 RELATED ID: 2GT2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE DBREF 2GT4 A 2 160 UNP P32056 NUDD_ECOLI 1 159 DBREF 2GT4 B 2 160 UNP P32056 NUDD_ECOLI 1 159 DBREF 2GT4 C 2 160 UNP P32056 NUDD_ECOLI 1 159 SEQADV 2GT4 MET A 1 UNP P32056 INITIATING METHIONINE SEQADV 2GT4 PHE A 103 UNP P32056 TYR 102 ENGINEERED MUTATION SEQADV 2GT4 MET B 1 UNP P32056 INITIATING METHIONINE SEQADV 2GT4 PHE B 103 UNP P32056 TYR 102 ENGINEERED MUTATION SEQADV 2GT4 MET C 1 UNP P32056 INITIATING METHIONINE SEQADV 2GT4 PHE C 103 UNP P32056 TYR 102 ENGINEERED MUTATION SEQRES 1 A 160 MET MET PHE LEU ARG GLN GLU ASP PHE ALA THR VAL VAL SEQRES 2 A 160 ARG SER THR PRO LEU VAL SER LEU ASP PHE ILE VAL GLU SEQRES 3 A 160 ASN SER ARG GLY GLU PHE LEU LEU GLY LYS ARG THR ASN SEQRES 4 A 160 ARG PRO ALA GLN GLY TYR TRP PHE VAL PRO GLY GLY ARG SEQRES 5 A 160 VAL GLN LYS ASP GLU THR LEU GLU ALA ALA PHE GLU ARG SEQRES 6 A 160 LEU THR MET ALA GLU LEU GLY LEU ARG LEU PRO ILE THR SEQRES 7 A 160 ALA GLY GLN PHE TYR GLY VAL TRP GLN HIS PHE TYR ASP SEQRES 8 A 160 ASP ASN PHE SER GLY THR ASP PHE THR THR HIS PHE VAL SEQRES 9 A 160 VAL LEU GLY PHE ARG PHE ARG VAL SER GLU GLU GLU LEU SEQRES 10 A 160 LEU LEU PRO ASP GLU GLN HIS ASP ASP TYR ARG TRP LEU SEQRES 11 A 160 THR SER ASP ALA LEU LEU ALA SER ASP ASN VAL HIS ALA SEQRES 12 A 160 ASN SER ARG ALA TYR PHE LEU ALA GLU LYS ARG THR GLY SEQRES 13 A 160 VAL PRO GLY LEU SEQRES 1 B 160 MET MET PHE LEU ARG GLN GLU ASP PHE ALA THR VAL VAL SEQRES 2 B 160 ARG SER THR PRO LEU VAL SER LEU ASP PHE ILE VAL GLU SEQRES 3 B 160 ASN SER ARG GLY GLU PHE LEU LEU GLY LYS ARG THR ASN SEQRES 4 B 160 ARG PRO ALA GLN GLY TYR TRP PHE VAL PRO GLY GLY ARG SEQRES 5 B 160 VAL GLN LYS ASP GLU THR LEU GLU ALA ALA PHE GLU ARG SEQRES 6 B 160 LEU THR MET ALA GLU LEU GLY LEU ARG LEU PRO ILE THR SEQRES 7 B 160 ALA GLY GLN PHE TYR GLY VAL TRP GLN HIS PHE TYR ASP SEQRES 8 B 160 ASP ASN PHE SER GLY THR ASP PHE THR THR HIS PHE VAL SEQRES 9 B 160 VAL LEU GLY PHE ARG PHE ARG VAL SER GLU GLU GLU LEU SEQRES 10 B 160 LEU LEU PRO ASP GLU GLN HIS ASP ASP TYR ARG TRP LEU SEQRES 11 B 160 THR SER ASP ALA LEU LEU ALA SER ASP ASN VAL HIS ALA SEQRES 12 B 160 ASN SER ARG ALA TYR PHE LEU ALA GLU LYS ARG THR GLY SEQRES 13 B 160 VAL PRO GLY LEU SEQRES 1 C 160 MET MET PHE LEU ARG GLN GLU ASP PHE ALA THR VAL VAL SEQRES 2 C 160 ARG SER THR PRO LEU VAL SER LEU ASP PHE ILE VAL GLU SEQRES 3 C 160 ASN SER ARG GLY GLU PHE LEU LEU GLY LYS ARG THR ASN SEQRES 4 C 160 ARG PRO ALA GLN GLY TYR TRP PHE VAL PRO GLY GLY ARG SEQRES 5 C 160 VAL GLN LYS ASP GLU THR LEU GLU ALA ALA PHE GLU ARG SEQRES 6 C 160 LEU THR MET ALA GLU LEU GLY LEU ARG LEU PRO ILE THR SEQRES 7 C 160 ALA GLY GLN PHE TYR GLY VAL TRP GLN HIS PHE TYR ASP SEQRES 8 C 160 ASP ASN PHE SER GLY THR ASP PHE THR THR HIS PHE VAL SEQRES 9 C 160 VAL LEU GLY PHE ARG PHE ARG VAL SER GLU GLU GLU LEU SEQRES 10 C 160 LEU LEU PRO ASP GLU GLN HIS ASP ASP TYR ARG TRP LEU SEQRES 11 C 160 THR SER ASP ALA LEU LEU ALA SER ASP ASN VAL HIS ALA SEQRES 12 C 160 ASN SER ARG ALA TYR PHE LEU ALA GLU LYS ARG THR GLY SEQRES 13 C 160 VAL PRO GLY LEU MODRES 2GT4 ASN C 39 ASN GLYCOSYLATION SITE MODRES 2GT4 ASN B 39 ASN GLYCOSYLATION SITE HET MG A 401 1 HET GDD A 201 39 HET BMA B 202 11 HET MG B 401 1 HET GDD B 201 39 HET BMA C 202 11 HET MG C 401 1 HET GDD C 201 39 HETNAM MG MAGNESIUM ION HETNAM GDD GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 MG 3(MG 2+) FORMUL 5 GDD 3(C16 H25 N5 O16 P2) FORMUL 6 BMA 2(C6 H12 O6) FORMUL 12 HOH *345(H2 O) HELIX 1 1 ARG A 5 THR A 16 1 12 HELIX 2 2 THR A 58 GLY A 72 1 15 HELIX 3 3 PRO A 76 GLY A 80 5 5 HELIX 4 4 SER A 113 LEU A 117 5 5 HELIX 5 5 PRO A 120 ASP A 125 5 6 HELIX 6 6 THR A 131 SER A 138 1 8 HELIX 7 7 HIS A 142 ALA A 147 1 6 HELIX 8 8 LEU A 150 THR A 155 1 6 HELIX 9 9 ARG B 5 THR B 16 1 12 HELIX 10 10 THR B 58 GLY B 72 1 15 HELIX 11 11 PRO B 76 GLY B 80 5 5 HELIX 12 12 SER B 113 LEU B 117 5 5 HELIX 13 13 ASP B 121 ASP B 125 5 5 HELIX 14 14 THR B 131 ALA B 137 1 7 HELIX 15 15 HIS B 142 ALA B 147 1 6 HELIX 16 16 LEU B 150 THR B 155 1 6 HELIX 17 17 ARG C 5 THR C 16 1 12 HELIX 18 18 THR C 58 LEU C 71 1 14 HELIX 19 19 PRO C 76 GLY C 80 5 5 HELIX 20 20 SER C 113 LEU C 117 5 5 HELIX 21 21 PRO C 120 ASP C 125 5 6 HELIX 22 22 THR C 131 ALA C 137 1 7 HELIX 23 23 HIS C 142 ALA C 147 1 6 HELIX 24 24 LEU C 150 THR C 155 1 6 SHEET 1 A 4 GLY A 50 ARG A 52 0 SHEET 2 A 4 LEU A 18 GLU A 26 -1 N LEU A 21 O GLY A 51 SHEET 3 A 4 THR A 101 ARG A 111 1 O VAL A 104 N LEU A 18 SHEET 4 A 4 GLN A 81 TYR A 90 -1 N TYR A 83 O GLY A 107 SHEET 1 B 3 TYR A 45 PHE A 47 0 SHEET 2 B 3 PHE A 32 ARG A 37 -1 N GLY A 35 O PHE A 47 SHEET 3 B 3 TYR A 127 LEU A 130 -1 O LEU A 130 N PHE A 32 SHEET 1 C 4 GLY B 50 ARG B 52 0 SHEET 2 C 4 LEU B 18 GLU B 26 -1 N LEU B 21 O GLY B 51 SHEET 3 C 4 THR B 101 ARG B 111 1 O HIS B 102 N LEU B 18 SHEET 4 C 4 GLN B 81 TYR B 90 -1 N TYR B 83 O GLY B 107 SHEET 1 D 3 TRP B 46 PHE B 47 0 SHEET 2 D 3 PHE B 32 LYS B 36 -1 N GLY B 35 O PHE B 47 SHEET 3 D 3 TYR B 127 LEU B 130 -1 O LEU B 130 N PHE B 32 SHEET 1 E 4 GLY C 50 ARG C 52 0 SHEET 2 E 4 LEU C 18 GLU C 26 -1 N LEU C 21 O GLY C 51 SHEET 3 E 4 THR C 101 ARG C 111 1 O HIS C 102 N LEU C 18 SHEET 4 E 4 GLN C 81 TYR C 90 -1 N TRP C 86 O VAL C 105 SHEET 1 F 3 TRP C 46 PHE C 47 0 SHEET 2 F 3 PHE C 32 LYS C 36 -1 N GLY C 35 O PHE C 47 SHEET 3 F 3 TYR C 127 LEU C 130 -1 O LEU C 130 N PHE C 32 LINK O GLY A 50 MG MG A 401 1555 1555 2.20 LINK OE2 GLU A 70 MG MG A 401 1555 1555 2.36 LINK O2B GDD A 201 MG MG A 401 1555 1555 2.60 LINK O2A GDD A 201 MG MG A 401 1555 1555 2.18 LINK MG MG A 401 O HOH A 411 1555 1555 2.36 LINK MG MG A 401 O HOH A 455 1555 1555 2.32 LINK O GLY B 50 MG MG B 401 1555 1555 2.19 LINK OE2 GLU B 70 MG MG B 401 1555 1555 2.18 LINK O2B GDD B 201 MG MG B 401 1555 1555 2.20 LINK O2A GDD B 201 MG MG B 401 1555 1555 2.18 LINK MG MG B 401 O HOH B 402 1555 1555 2.29 LINK MG MG B 401 O HOH B 417 1555 1555 1.92 LINK O GLY C 50 MG MG C 401 1555 1555 2.17 LINK OE2 GLU C 70 MG MG C 401 1555 1555 2.18 LINK O2B GDD C 201 MG MG C 401 1555 1555 2.17 LINK O2A GDD C 201 MG MG C 401 1555 1555 2.19 LINK O4 BMA C 202 MG MG C 401 1555 1555 3.12 LINK MG MG C 401 O HOH C 413 1555 1555 2.66 LINK MG MG C 401 O HOH C 425 1555 1555 2.37 CISPEP 1 ARG A 40 PRO A 41 0 -1.65 CISPEP 2 ARG B 40 PRO B 41 0 -2.86 CISPEP 3 ARG C 40 PRO C 41 0 -0.68 CRYST1 137.785 93.893 66.103 90.00 91.23 90.00 C 1 2 1 12 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 0.007258 0.000000 0.000156 0.00000 SCALE2 0.000000 0.010650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015131 0.00000