HEADER HYDROLASE 20-DEC-03 1RYA TITLE CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN TITLE 2 COMPLEX WITH GDP AND MG COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-MANNOSE MANNOSYL HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GDPMH, COLANIC ACID BIOSYNTHESIS PROTEIN WCAH; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NUDD, WCAH, GMM, B2051; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11B KEYWDS GDP-MANNOSE, MANNOSE, GDP-GLUCOSE, NUDIX, NUDIX MG-COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.GABELLI,M.A.BIANCHET,P.M.LEGLER,A.S.MILDVAN,L.M.AMZEL REVDAT 6 14-FEB-24 1RYA 1 REMARK LINK REVDAT 5 04-APR-18 1RYA 1 REMARK REVDAT 4 31-JAN-18 1RYA 1 REMARK REVDAT 3 24-FEB-09 1RYA 1 VERSN REVDAT 2 29-JUN-04 1RYA 1 JRNL AUTHOR REVDAT 1 22-JUN-04 1RYA 0 JRNL AUTH S.B.GABELLI,M.A.BIANCHET,H.F.AZURMENDI,Z.XIA,V.SARAWAT, JRNL AUTH 2 A.S.MILDVAN,L.M.AMZEL JRNL TITL STRUCTURE AND MECHANISM OF GDP-MANNOSE GLYCOSYL HYDROLASE, A JRNL TITL 2 NUDIX ENZYME THAT CLEAVES AT CARBON INSTEAD OF PHOSPHORUS. JRNL REF STRUCTURE V. 12 927 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15274914 JRNL DOI 10.1016/J.STR.2004.03.028 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 88143 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4715 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4646 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 247 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 727 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : -0.03000 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): 0.049 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.657 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2748 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2398 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3738 ; 1.557 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5532 ; 0.847 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 7.737 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 392 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3046 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 634 ; 0.016 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 487 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2836 ; 0.261 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1616 ; 0.081 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 569 ; 0.146 ; 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): 14 ; 0.145 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 90 ; 0.367 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 64 ; 0.190 ; 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): 1594 ; 0.770 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2558 ; 1.416 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1154 ; 1.967 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 3.016 ; 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 : 1.40 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 1RYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 180; NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X6A; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791; 1.54 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 63.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE, AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M NA (OR MG) ACETATE, REMARK 280 0.1M TRIS HCL PH8.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.03450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.48700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.68150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.48700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.03450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.68150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE BIOLOGICAL ASSEMPLY IS THE DIMER PRESENT IN THE REMARK 300 ASYMMETRIC UNIT. 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: 5220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 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 CG MET A 68 O HOH A 1337 2.07 REMARK 500 O HOH B 1105 O HOH B 1358 2.10 REMARK 500 O ALA A 147 O HOH A 1338 2.13 REMARK 500 O HOH A 1073 O HOH A 1359 2.14 REMARK 500 OE1 GLU A 115 O HOH A 1358 2.17 REMARK 500 O HOH B 1096 O HOH B 1355 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 138 O HOH A 1356 2564 1.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 52 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP B 125 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 LEU B 150 N - CA - C ANGL. DEV. = -17.5 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 MET A 2 92.68 -169.46 REMARK 500 MET B 2 91.32 -167.47 REMARK 500 ALA B 151 -87.13 -169.65 REMARK 500 GLU B 152 100.75 177.78 REMARK 500 LYS B 153 44.90 -102.40 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 PHE B 149 LEU B 150 146.31 REMARK 500 LEU B 150 ALA B 151 -31.86 REMARK 500 GLU B 152 LYS B 153 143.46 REMARK 500 REMARK 500 REMARK: NULL 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE2 83.8 REMARK 620 3 GLN A 123 OE1 169.4 90.2 REMARK 620 4 GDP A 770 O3B 91.5 174.9 94.7 REMARK 620 5 GDP A 770 O2A 99.2 89.1 89.5 89.7 REMARK 620 6 HOH A1002 O 86.2 87.2 84.8 94.4 173.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 50 O REMARK 620 2 GLU B 70 OE2 84.8 REMARK 620 3 GLN B 123 OE1 170.7 90.2 REMARK 620 4 GDP B 771 O3B 91.8 176.6 93.1 REMARK 620 5 GDP B 771 O2A 98.6 90.7 89.2 90.1 REMARK 620 6 HOH B1004 O 86.6 85.4 85.2 94.1 173.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 770 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 771 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 870 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 871 DBREF 1RYA A 1 160 UNP P32056 NUDD_ECOLI 1 160 DBREF 1RYA B 1 160 UNP P32056 NUDD_ECOLI 1 160 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 TYR 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 TYR 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 HET MG A1001 1 HET GDP A 770 28 HET TRS A 870 8 HET MG B1002 1 HET CL B1003 1 HET GDP B 771 28 HET TRS B 871 8 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CL CHLORIDE ION HETSYN TRS TRIS BUFFER FORMUL 3 MG 2(MG 2+) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 5 TRS 2(C4 H12 N O3 1+) FORMUL 7 CL CL 1- FORMUL 10 HOH *727(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 THR A 131 SER A 138 1 8 HELIX 6 6 HIS A 142 ALA A 147 1 6 HELIX 7 7 LEU A 150 THR A 155 1 6 HELIX 8 8 ARG B 5 THR B 16 1 12 HELIX 9 9 THR B 58 GLY B 72 1 15 HELIX 10 10 PRO B 76 GLY B 80 5 5 HELIX 11 11 SER B 113 LEU B 117 5 5 HELIX 12 12 THR B 131 SER B 138 1 8 HELIX 13 13 HIS B 142 ALA B 147 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 HIS A 102 N LEU A 18 SHEET 4 A 4 GLN A 81 TYR A 90 -1 N TYR A 90 O THR A 101 SHEET 1 B 3 TRP A 46 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 HIS A 124 LEU A 130 -1 O ARG A 128 N LEU A 34 SHEET 1 C 5 GLY B 50 ARG B 52 0 SHEET 2 C 5 LEU B 18 GLU B 26 -1 N LEU B 21 O GLY B 51 SHEET 3 C 5 THR B 101 ARG B 111 1 O HIS B 102 N LEU B 18 SHEET 4 C 5 GLN B 81 TYR B 90 -1 N TRP B 86 O VAL B 105 SHEET 5 C 5 THR B 155 PRO B 158 -1 O THR B 155 N VAL B 85 SHEET 1 D 3 TRP B 46 PHE B 47 0 SHEET 2 D 3 PHE B 32 ARG B 37 -1 N GLY B 35 O PHE B 47 SHEET 3 D 3 HIS B 124 LEU B 130 -1 O LEU B 130 N PHE B 32 LINK O GLY A 50 MG MG A1001 1555 1555 2.07 LINK OE2 GLU A 70 MG MG A1001 1555 1555 2.07 LINK OE1 GLN A 123 MG MG A1001 1555 1555 2.16 LINK O3B GDP A 770 MG MG A1001 1555 1555 2.05 LINK O2A GDP A 770 MG MG A1001 1555 1555 2.05 LINK MG MG A1001 O HOH A1002 1555 1555 2.11 LINK O GLY B 50 MG MG B1002 1555 1555 2.05 LINK OE2 GLU B 70 MG MG B1002 1555 1555 2.06 LINK OE1 GLN B 123 MG MG B1002 1555 1555 2.12 LINK O3B GDP B 771 MG MG B1002 1555 1555 2.03 LINK O2A GDP B 771 MG MG B1002 1555 1555 2.07 LINK MG MG B1002 O HOH B1004 1555 1555 2.11 CISPEP 1 ARG A 40 PRO A 41 0 -4.55 CISPEP 2 ARG B 40 PRO B 41 0 -6.00 SITE 1 AC1 5 GLY A 50 GLU A 70 GLN A 123 GDP A 770 SITE 2 AC1 5 HOH A1002 SITE 1 AC2 5 GLY B 50 GLU B 70 GLN B 123 GDP B 771 SITE 2 AC2 5 HOH B1004 SITE 1 AC3 2 SER B 28 GLU B 114 SITE 1 AC4 25 PHE A 3 LEU A 4 PHE A 9 ARG A 37 SITE 2 AC4 25 ASN A 39 GLY A 50 GLY A 51 ARG A 52 SITE 3 AC4 25 GLU A 70 PHE A 94 TYR A 103 GLN A 123 SITE 4 AC4 25 TRS A 870 MG A1001 HOH A1002 HOH A1003 SITE 5 AC4 25 HOH A1010 HOH A1018 HOH A1040 HOH A1075 SITE 6 AC4 25 HOH A1078 HOH A1102 HOH A1103 HOH A1132 SITE 7 AC4 25 HOH A1153 SITE 1 AC5 25 PHE B 3 LEU B 4 PHE B 9 ARG B 37 SITE 2 AC5 25 ASN B 39 GLY B 50 GLY B 51 ARG B 52 SITE 3 AC5 25 GLU B 70 PHE B 94 TYR B 103 GLN B 123 SITE 4 AC5 25 TRS B 871 MG B1002 HOH B1004 HOH B1006 SITE 5 AC5 25 HOH B1007 HOH B1012 HOH B1034 HOH B1067 SITE 6 AC5 25 HOH B1082 HOH B1135 HOH B1164 HOH B1179 SITE 7 AC5 25 HOH B1189 SITE 1 AC6 9 SER A 20 ASP A 22 ARG A 37 PHE A 47 SITE 2 AC6 9 HIS A 88 TYR A 90 TYR A 103 GDP A 770 SITE 3 AC6 9 HOH A1005 SITE 1 AC7 9 SER B 20 ASP B 22 ARG B 37 PHE B 47 SITE 2 AC7 9 HIS B 88 TYR B 90 TYR B 103 GDP B 771 SITE 3 AC7 9 HOH B1009 CRYST1 50.069 81.363 98.974 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010104 0.00000