HEADER TRANSFERASE 17-FEB-09 3GAH TITLE STRUCTURE OF A F112H VARIANT PDUO-TYPE ATP:CORRINOID TITLE 2 ADENOSYLTRANSFERASE FROM LACTOBACILLUS REUTERI COMPLEXED WITH TITLE 3 COBALAMIN 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; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS REUTERI; SOURCE 3 ORGANISM_TAXID: 1598; SOURCE 4 STRAIN: CRL1098; SOURCE 5 GENE: COBA, PDUO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ST MAURICE,P.E.MERA,J.C.ESCALANTE-SEMERENA,I.RAYMENT REVDAT 5 21-FEB-24 3GAH 1 REMARK REVDAT 4 20-OCT-21 3GAH 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3GAH 1 REMARK REVDAT 2 24-OCT-12 3GAH 1 FORMUL VERSN REVDAT 1 07-JUL-09 3GAH 0 JRNL AUTH P.E.MERA,M.ST MAURICE,I.RAYMENT,J.C.ESCALANTE-SEMERENA JRNL TITL RESIDUE PHE112 OF THE HUMAN-TYPE CORRINOID JRNL TITL 2 ADENOSYLTRANSFERASE (PDUO) ENZYME OF LACTOBACILLUS REUTERI JRNL TITL 3 IS CRITICAL TO THE FORMATION OF THE FOUR-COORDINATE CO(II) JRNL TITL 4 CORRINOID SUBSTRATE AND TO THE ACTIVITY OF THE ENZYME. JRNL REF BIOCHEMISTRY V. 48 3138 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19236001 JRNL DOI 10.1021/BI9000134 REMARK 2 REMARK 2 RESOLUTION. 1.17 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 73249 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3689 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) : 1.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4974 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 239 REMARK 3 BIN FREE R VALUE : 0.2030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1511 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.05000 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): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.448 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1838 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2558 ; 2.849 ; 2.059 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 206 ; 5.841 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;33.162 ;24.607 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 289 ;11.727 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.782 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 274 ; 0.370 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1446 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 931 ; 0.252 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1322 ; 0.323 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.193 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.107 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 91 ; 0.249 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 47 ; 0.320 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.074 ; 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): 1005 ; 1.043 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1640 ; 1.801 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 839 ; 2.651 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 918 ; 3.616 ; 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 3GAH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73398 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.4780 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.17900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ANOXIC, 14% PEG 8000, 0.2M POTASSIUM REMARK 280 CHLORIDE, 0.1 M HEPPS, 30 UG/ML E. COLI FMN REDUCTASE, 50 MM REMARK 280 NADH, 10 MM FMN, 10 MM HYDOXYCOBALAMIN, 10 MM ATP, 10 MM REMARK 280 MAGNESIUM CHLORIDE, 0.3 M SODIUM CHLORIDE , PH 8.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 40.40700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.32899 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.83067 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 40.40700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.32899 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.83067 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 40.40700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.32899 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.83067 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.65798 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.66133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.65798 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 59.66133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.65798 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 59.66133 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 TRIMER IS GENERATED BY THE FOLLOWING SYMMETRY REMARK 300 OPERATIONS: [-Y, X-Y, Z + (0 0 0)] AND [-X+Y, -X, Z + (0 0 0)] 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: 18640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 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 0.00000 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 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 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 A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 383 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 VAL A 1 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 GLU A 80 CD OE1 OE2 REMARK 470 LYS A 87 CE NZ REMARK 470 GLU A 89 CD OE1 OE2 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 ASN A 101 ND2 REMARK 480 LYS A 110 CD CE NZ 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 N LYS A 184 O HOH A 384 1.75 REMARK 500 O58 B12 A 800 O HOH A 292 1.91 REMARK 500 O HOH A 201 O HOH A 208 2.16 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 O HOH A 216 O HOH A 219 2555 1.30 REMARK 500 O HOH A 217 O HOH A 218 2555 1.46 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 14 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 GLU A 33 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MET A 178 CG - SD - CE ANGL. DEV. = -10.8 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 18 -4.57 79.24 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 B12 A 800 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 191 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 3 O REMARK 620 2 ATP A 999 O1G 87.5 REMARK 620 3 ATP A 999 O2G 135.2 53.2 REMARK 620 4 ATP A 999 O2A 118.0 90.7 86.4 REMARK 620 5 ATP A 999 O1A 165.1 95.5 55.0 47.5 REMARK 620 N 1 2 3 4 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 PRO A 76 O REMARK 620 2 ALA A 77 O 74.9 REMARK 620 3 ASP A 79 O 92.4 98.9 REMARK 620 4 HIS A 82 O 111.8 172.3 77.5 REMARK 620 5 HOH A 297 O 159.1 84.7 95.3 88.9 REMARK 620 6 HOH A 300 O 95.3 86.9 171.4 96.0 78.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 189 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 192 O REMARK 620 2 HOH A 193 O 95.4 REMARK 620 3 ATP A 999 O2G 172.6 92.0 REMARK 620 4 ATP A 999 O1B 87.0 175.8 85.8 REMARK 620 5 ATP A 999 O1A 89.0 87.6 92.0 89.0 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 ATP A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 191 DBREF 3GAH A 2 188 UNP Q50EJ2 Q50EJ2_LACRE 2 188 SEQADV 3GAH GLY A -5 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH ALA A -4 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH SER A -3 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH ALA A -2 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH PRO A -1 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH MET A 0 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH VAL A 1 UNP Q50EJ2 EXPRESSION TAG SEQADV 3GAH HIS A 112 UNP Q50EJ2 PHE 112 ENGINEERED MUTATION 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 HIS 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 ATP A 999 31 HET B12 A 800 132 HET MG A 189 1 HET MG A 190 1 HET K A 191 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM B12 COBALAMIN HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 B12 C62 H89 CO N13 O14 P 2+ FORMUL 4 MG 2(MG 2+) FORMUL 6 K K 1+ FORMUL 7 HOH *210(H2 O) HELIX 1 1 ASP A 25 LEU A 47 1 23 HELIX 2 2 THR A 52 VAL A 54 5 3 HELIX 3 3 LEU A 55 ALA A 74 1 20 HELIX 4 4 GLN A 88 VAL A 106 1 19 HELIX 5 5 THR A 118 GLU A 145 1 28 HELIX 6 6 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 191 1555 1555 2.61 LINK O PRO A 76 MG MG A 190 1555 1555 2.77 LINK O ALA A 77 MG MG A 190 1555 1555 2.89 LINK O AASP A 79 MG MG A 190 1555 1555 2.72 LINK O HIS A 82 MG MG A 190 1555 1555 2.57 LINK MG MG A 189 O HOH A 192 1555 1555 2.10 LINK MG MG A 189 O HOH A 193 1555 1555 2.04 LINK MG MG A 189 O2G ATP A 999 1555 1555 2.04 LINK MG MG A 189 O1B ATP A 999 1555 1555 2.10 LINK MG MG A 189 O1A ATP A 999 1555 1555 2.02 LINK MG MG A 190 O HOH A 297 1555 1555 2.80 LINK MG MG A 190 O HOH A 300 1555 1555 2.71 LINK K K A 191 O1G ATP A 999 1555 1555 2.84 LINK K K A 191 O2G ATP A 999 1555 1555 2.78 LINK K K A 191 O2A ATP A 999 1555 1555 2.74 LINK K K A 191 O1A ATP A 999 1555 1555 3.42 SITE 1 AC1 21 THR A 5 LYS A 6 ASN A 7 GLY A 8 SITE 2 AC1 21 THR A 13 ARG A 14 LYS A 23 VAL A 28 SITE 3 AC1 21 TYR A 31 ARG A 132 GLU A 135 ARG A 136 SITE 4 AC1 21 ASN A 156 MG A 189 K A 191 HOH A 192 SITE 5 AC1 21 HOH A 193 HOH A 194 HOH A 240 HOH A 258 SITE 6 AC1 21 B12 A 800 SITE 1 AC2 26 LYS A 2 ILE A 3 THR A 5 ARG A 14 SITE 2 AC2 26 ILE A 15 TYR A 31 ASP A 35 PHE A 67 SITE 3 AC2 26 GLY A 70 HIS A 71 HIS A 112 ILE A 113 SITE 4 AC2 26 ARG A 128 ARG A 132 SER A 159 ASP A 160 SITE 5 AC2 26 PHE A 163 VAL A 186 PHE A 187 K A 191 SITE 6 AC2 26 HOH A 268 HOH A 292 HOH A 332 HOH A 375 SITE 7 AC2 26 HOH A 395 ATP A 999 SITE 1 AC3 4 ASN A 156 HOH A 192 HOH A 193 ATP A 999 SITE 1 AC4 6 PRO A 76 ALA A 77 ASP A 79 HIS A 82 SITE 2 AC4 6 HOH A 297 HOH A 300 SITE 1 AC5 4 ILE A 3 ASP A 160 B12 A 800 ATP A 999 CRYST1 80.814 80.814 89.492 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 0.012374 0.007144 0.000000 0.00000 SCALE2 0.000000 0.014288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011174 0.00000