HEADER TRANSFERASE 10-MAR-08 3CI4 TITLE STRUCTURE OF THE PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFERASE FROM TITLE 2 LACTOBACILLUS REUTERI COMPLEXED WITH FOUR-COORDINATE COB(II)INAMIDE TITLE 3 AND ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: COBALAMIN ADENOSYLTRANSFERASE PDUO-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS REUTERI; SOURCE 3 STRAIN: CRL1098; SOURCE 4 GENE: COBA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ADENOSYLTRANSFERASE VARIANT, ATP BINDING, CORRIN BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ST.MAURICE,P.E.MERA,J.C.ESCALANTE-SEMERENA,I.RAYMENT REVDAT 3 21-FEB-24 3CI4 1 REMARK SEQADV REVDAT 2 24-FEB-09 3CI4 1 VERSN REVDAT 1 27-MAY-08 3CI4 0 JRNL AUTH M.ST MAURICE,P.MERA,K.PARK,T.C.BRUNOLD, JRNL AUTH 2 J.C.ESCALANTE-SEMERENA,I.RAYMENT JRNL TITL STRUCTURAL CHARACTERIZATION OF A HUMAN-TYPE CORRINOID JRNL TITL 2 ADENOSYLTRANSFERASE CONFIRMS THAT COENZYME B12 IS JRNL TITL 3 SYNTHESIZED THROUGH A FOUR-COORDINATE INTERMEDIATE. JRNL REF BIOCHEMISTRY V. 47 5755 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18452306 JRNL DOI 10.1021/BI800132D REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 12024 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 622 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 756 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1474 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : NULL 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): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.579 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1615 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2225 ; 1.993 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 186 ;10.019 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;34.657 ;24.605 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 244 ;12.043 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.220 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 247 ; 0.197 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1237 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 766 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1130 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 84 ; 0.116 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.078 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 85 ; 0.233 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.131 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.094 ; 0.200 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): 933 ; 0.570 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1501 ; 0.993 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 692 ; 1.724 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 724 ; 2.523 ; 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 : 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 3CI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MONTEL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13603 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ANOXIC, 13% PEG 8000, 0.1 M MES, 200 REMARK 280 MM KCL, 33 UG/ML FMN REDUCTASE, 20 MM NADH, 2 MM FMN, 2 MM REMARK 280 DICYANOCOBINAMIDE, 2 MM MGCL2, 2 MM ATP, PH 6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.91300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.57968 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.08667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 33.91300 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 19.57968 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.08667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 33.91300 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 19.57968 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.08667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.15936 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 74.17333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 39.15936 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 74.17333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 39.15936 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 74.17333 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.500000 -0.866025 0.000000 67.82600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 33.91300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 58.73904 REMARK 350 BIOMT3 3 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 A1059 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1061 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 GLY A -5 REMARK 465 ALA A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 PRO A -1 REMARK 465 MET A 0 REMARK 465 ARG A 188 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 VAL A 1 CB CG1 CG2 REMARK 470 LYS A 2 CE NZ REMARK 470 LYS A 10 CD CE NZ REMARK 470 ARG A 14 CZ NH1 NH2 REMARK 470 LYS A 18 CE NZ REMARK 470 LYS A 45 NZ REMARK 470 GLU A 80 CB CG CD OE1 OE2 REMARK 470 ARG A 81 CD NE CZ NH1 NH2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 LYS A 87 CE NZ REMARK 470 GLU A 89 CD OE1 OE2 REMARK 470 GLN A 90 CD OE1 NE2 REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 GLN A 104 CG CD OE1 NE2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 GLN A 140 OE1 NE2 REMARK 470 MET A 178 CG SD CE REMARK 470 LYS A 184 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 105 CA CB CG1 CG2 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 LYS A 110 N - CA - C ANGL. DEV. = 19.7 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 LYS A 6 -0.72 71.24 REMARK 500 ILE A 15 -168.41 -104.13 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 VAL A 109 LYS A 110 118.33 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 K A 189 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 3 O REMARK 620 2 ATP A 999 O2A 112.8 REMARK 620 3 ATP A 999 O1G 83.3 93.2 REMARK 620 4 ATP A 999 O2G 130.1 94.2 52.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 190 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 999 O1A REMARK 620 2 ATP A 999 O2G 90.2 REMARK 620 3 ATP A 999 O1B 89.3 86.6 REMARK 620 4 HOH A1073 O 87.4 92.7 176.6 REMARK 620 5 HOH A1074 O 88.1 169.8 83.4 97.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CBY A 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NT8 RELATED DB: PDB REMARK 900 ATP BOUND AT THE ACTIVE SITE OF A PDUO TYPE ATP:CO(I) REMARK 900 RELATED ID: 3CI3 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFERASE REMARK 900 FROM LACTOBACILLUS REUTERI COMPLEXED WITH PARTIAL ADENOSYLCOBALAMIN REMARK 900 AND PPPI REMARK 900 RELATED ID: 3CI1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFERASE REMARK 900 FROM LACTOBACILLUS REUTERI COMPLEXED WITH FOUR-COORDINATE COB(II) REMARK 900 ALAMIN AND ATP DBREF 3CI4 A 2 188 UNP Q50EJ2 Q50EJ2_LACRE 2 188 SEQADV 3CI4 GLY A -5 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 ALA A -4 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 SER A -3 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 ALA A -2 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 PRO A -1 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 MET A 0 UNP Q50EJ2 EXPRESSION TAG SEQADV 3CI4 VAL A 1 UNP Q50EJ2 EXPRESSION TAG SEQRES 1 A 194 GLY ALA SER ALA PRO MET VAL LYS ILE TYR THR LYS ASN SEQRES 2 A 194 GLY ASP LYS GLY GLN THR ARG ILE ILE GLY LYS GLN ILE SEQRES 3 A 194 LEU TYR LYS ASN ASP PRO ARG VAL ALA ALA TYR GLY GLU SEQRES 4 A 194 VAL ASP GLU LEU ASN SER TRP VAL GLY TYR THR LYS SER SEQRES 5 A 194 LEU ILE ASN SER HIS THR GLN VAL LEU SER ASN GLU LEU SEQRES 6 A 194 GLU GLU ILE GLN GLN LEU LEU PHE ASP CYS GLY HIS ASP SEQRES 7 A 194 LEU ALA THR PRO ALA ASP ASP GLU ARG HIS SER PHE LYS SEQRES 8 A 194 PHE LYS GLN GLU GLN PRO THR VAL TRP LEU GLU GLU LYS SEQRES 9 A 194 ILE ASP ASN TYR THR GLN VAL VAL PRO ALA VAL LYS LYS SEQRES 10 A 194 PHE ILE LEU PRO GLY GLY THR GLN LEU ALA SER ALA LEU SEQRES 11 A 194 HIS VAL ALA ARG THR ILE THR ARG ARG ALA GLU ARG GLN SEQRES 12 A 194 ILE VAL GLN LEU MET ARG GLU GLU GLN ILE ASN GLN ASP SEQRES 13 A 194 VAL LEU ILE PHE ILE ASN ARG LEU SER ASP TYR PHE PHE SEQRES 14 A 194 ALA ALA ALA ARG TYR ALA ASN TYR LEU GLU GLN GLN PRO SEQRES 15 A 194 ASP MET LEU TYR ARG ASN SER LYS ASP VAL PHE ARG HET K A 189 1 HET MG A 190 1 HET ATP A 999 31 HET CBY A 800 68 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CBY COB(II)INAMIDE FORMUL 2 K K 1+ FORMUL 3 MG MG 2+ FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 CBY C48 H72 CO N11 O8 1+ FORMUL 6 HOH *85(H2 O) HELIX 1 1 LYS A 6 LYS A 10 5 5 HELIX 2 2 ASP A 25 SER A 46 1 22 HELIX 3 3 THR A 52 VAL A 54 5 3 HELIX 4 4 LEU A 55 ALA A 74 1 20 HELIX 5 5 GLN A 88 VAL A 106 1 19 HELIX 6 6 THR A 118 ARG A 143 1 26 HELIX 7 7 ASN A 148 GLU A 173 1 26 SHEET 1 A 2 GLN A 12 ARG A 14 0 SHEET 2 A 2 ILE A 20 TYR A 22 -1 O LEU A 21 N THR A 13 LINK O ILE A 3 K K A 189 1555 1555 2.74 LINK K K A 189 O2A ATP A 999 1555 1555 2.89 LINK K K A 189 O1G ATP A 999 1555 1555 2.88 LINK K K A 189 O2G ATP A 999 1555 1555 2.68 LINK MG MG A 190 O1A ATP A 999 1555 1555 2.05 LINK MG MG A 190 O2G ATP A 999 1555 1555 2.06 LINK MG MG A 190 O1B ATP A 999 1555 1555 2.16 LINK MG MG A 190 O HOH A1073 1555 1555 1.94 LINK MG MG A 190 O HOH A1074 1555 1555 2.25 SITE 1 AC1 4 ILE A 3 ASP A 160 CBY A 800 ATP A 999 SITE 1 AC2 4 ASN A 156 ATP A 999 HOH A1073 HOH A1074 SITE 1 AC3 22 THR A 5 LYS A 6 ASN A 7 GLY A 8 SITE 2 AC3 22 THR A 13 ARG A 14 LYS A 23 VAL A 28 SITE 3 AC3 22 TYR A 31 ARG A 132 GLU A 135 ARG A 136 SITE 4 AC3 22 ASN A 156 ASP A 160 K A 189 MG A 190 SITE 5 AC3 22 CBY A 800 HOH A1063 HOH A1071 HOH A1073 SITE 6 AC3 22 HOH A1074 HOH A1075 SITE 1 AC4 23 LYS A 2 ILE A 3 THR A 5 ARG A 14 SITE 2 AC4 23 ILE A 15 TYR A 31 ASP A 35 GLY A 70 SITE 3 AC4 23 HIS A 71 PHE A 112 ILE A 113 ARG A 128 SITE 4 AC4 23 ARG A 132 SER A 159 ASP A 160 PHE A 163 SITE 5 AC4 23 VAL A 186 PHE A 187 K A 189 ATP A 999 SITE 6 AC4 23 HOH A1014 HOH A1070 HOH A1079 CRYST1 67.826 67.826 111.260 90.00 90.00 120.00 H 3 9 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 0.014744 0.008512 0.000000 0.00000 SCALE2 0.000000 0.017024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008988 0.00000