HEADER TRANSFERASE 16-JAN-02 1GTK TITLE TIME-RESOLVED AND STATIC-ENSEMBLE STRUCTURAL CHEMISTRY OF TITLE 2 HYDROXYMETHYLBILANE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THREE DOMAINS; COMPND 5 SYNONYM: HYDROXYMETHYLBILANE SYNTHASE, PBG, HMBS, HYDROXYMETHYLBILANE COMPND 6 SYNTHASE, PRE-UROPORPHYRINOGEN SYNTHASE; COMPND 7 EC: 2.5.1.61; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE COMPND 10 242 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, BIOSYNTHESIS OF LINEAR TETRAPYRROLE, ALL ALPHA/BETA EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HELLIWELL,Y.P.NIEH,J.RAFTERY,A.CASSETTA,J.HABASH,P.D.CARR, AUTHOR 2 T.URSBY,M.WULFF,A.W.THOMPSON,A.C.NIEMANN,A.HAEDENER REVDAT 10 13-DEC-23 1GTK 1 REMARK REVDAT 9 08-MAY-19 1GTK 1 REMARK LINK REVDAT 8 25-SEP-13 1GTK 1 HEADER KEYWDS REMARK HETNAM REVDAT 7 27-JUL-11 1GTK 1 COMPND REVDAT 6 13-JUL-11 1GTK 1 VERSN REVDAT 5 24-FEB-09 1GTK 1 VERSN REVDAT 4 13-FEB-03 1GTK 1 JRNL REVDAT 3 06-FEB-03 1GTK 1 JRNL REMARK REVDAT 2 24-JAN-03 1GTK 1 REMARK REVDAT 1 16-JAN-03 1GTK 0 JRNL AUTH J.R.HELLIWELL,Y.P.NIEH,J.HABASH,P.F.FAULDER,J.RAFTERY, JRNL AUTH 2 M.CIANCI,M.WULFF,A.HADENER JRNL TITL TIME-RESOLVED AND STATIC-ENSEMBLE STRUCTURAL CHEMISTRY OF JRNL TITL 2 HYDROXYMETHYLBILANE SYNTHASE JRNL REF FARADAY DISCUSS. V. 122 131 2003 JRNL REFN ISSN 1359-6640 JRNL PMID 12555854 JRNL DOI 10.1039/B201331B REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.HELLIWELL,Y.P.NIEH,J.RAFTERY,A.CASSETTA,J.HABASH, REMARK 1 AUTH 2 P.D.CARR,T.URSBY,M.WULFF,A.W.THOMPSON,A.C.NIEMANN,A.HADENER REMARK 1 TITL TIME-RESOLVED STRUCTURES OF HYDROXYMETHYLBILANE SYNTHASE REMARK 1 TITL 2 (LYS59GLN MUTANT) AS IT IS LOADED WITH SUBSTRATE IN THE REMARK 1 TITL 3 CRYSTAL DETERMINED BY LAUE DIFFRACTION REMARK 1 REF J.CHEM.SOC.,FARADAY TRANS. V. 94 2615 1998 REMARK 1 REFN ISSN 0956-5000 REMARK 1 DOI 10.1039/A802217H REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 32708 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1709 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1555 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.946 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2287 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2164 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 3099 ; 2.004 ; 1.995 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 4999 ; 0.980 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2573 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 435 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 484 ; 0.281 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2062 ; 0.218 ; 0.300 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): 202 ; 0.173 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.141 ; 0.500 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): 11 ; 0.304 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.292 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.262 ; 0.500 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): 1458 ; 1.174 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2329 ; 1.982 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 829 ; 3.140 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 770 ; 4.704 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 313 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4635 -1.0970 21.7791 REMARK 3 T TENSOR REMARK 3 T11: 0.0230 T22: 0.0244 REMARK 3 T33: 0.0080 T12: 0.0057 REMARK 3 T13: 0.0077 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.1975 L22: 0.8669 REMARK 3 L33: 0.2831 L12: -0.0705 REMARK 3 L13: 0.1190 L23: -0.2144 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: 0.0056 S13: 0.0049 REMARK 3 S21: 0.0502 S22: 0.0089 S23: -0.0016 REMARK 3 S31: -0.0099 S32: 0.0120 S33: -0.0090 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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. THE ASYMMETRIC UNIT OF THIS STRUCTURE IS NOT REMARK 3 COMPLETE.RESIDUES 1-2, 43-59 ARE MISSING IN THE ENTRY. REMARK 4 REMARK 4 1GTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1290009254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID09 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8611 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 43.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.7 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 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: O REMARK 200 STARTING MODEL: PDB ENTRY 2YPN REMARK 200 REMARK 200 REMARK: THE STRUCTURE WAS ALREADY DETERMINED BUT REFINED HERE ONLY REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLISED AT PH 5.3 IN REMARK 280 SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, REMARK 280 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M REMARK 280 SODIUM ACETATE., PH 5.30, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 43.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.95000 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 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 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 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 1 REMARK 465 LEU A 2 REMARK 465 THR A 43 REMARK 465 ARG A 44 REMARK 465 GLY A 45 REMARK 465 ASP A 46 REMARK 465 VAL A 47 REMARK 465 ILE A 48 REMARK 465 LEU A 49 REMARK 465 ASP A 50 REMARK 465 THR A 51 REMARK 465 PRO A 52 REMARK 465 LEU A 53 REMARK 465 ALA A 54 REMARK 465 LYS A 55 REMARK 465 VAL A 56 REMARK 465 GLY A 57 REMARK 465 GLY A 58 REMARK 465 LYS A 59 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 LEU A 61 CG CD1 CD2 REMARK 470 PHE A 62 CG CD1 CD2 CE1 CE2 CZ 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 O ASP A 3 NH1 ARG A 211 1.99 REMARK 500 CD ARG A 227 O ALA A 250 2.01 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 2139 O HOH A 2139 2655 2.09 REMARK 500 O HOH A 2004 O HOH A 2011 3556 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 82 SD MET A 82 CE -0.363 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 ASP A 25 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 114 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 208 CB - CG - OD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 227 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 227 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = -6.1 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 ASN A 4 6.81 -39.75 REMARK 500 MET A 41 -169.62 -165.29 REMARK 500 LEU A 61 -94.10 76.96 REMARK 500 THR A 127 141.48 -175.57 REMARK 500 ASN A 308 90.05 56.20 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 A2004 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A2011 DISTANCE = 8.18 ANGSTROMS REMARK 525 HOH A2026 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2027 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A2033 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2063 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A2081 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A2152 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 6.12 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DPM A 315 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AH5 RELATED DB: PDB REMARK 900 REDUCED FORM SELENOMETHIONINE-LABELLED HYDROXYMETHYLBILANE SYNTHASE REMARK 900 DETERMINED BY MAD REMARK 900 RELATED ID: 1YPN RELATED DB: PDB REMARK 900 REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL REMARK 900 STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED REMARK 900 LAUE DIFFRACTION REMARK 900 RELATED ID: 2YPN RELATED DB: PDB REMARK 900 REDUCED FORM HYDROXYLMETHYLBILANE SYNTHASE CRYSTAL STRUCTURE DBREF 1GTK A 1 313 UNP P06983 HEM3_ECOLI 1 313 SEQRES 1 A 313 MET LEU ASP ASN VAL LEU ARG ILE ALA THR ARG GLN SER SEQRES 2 A 313 PRO LEU ALA LEU TRP GLN ALA HIS TYR VAL LYS ASP LYS SEQRES 3 A 313 LEU MET ALA SER HIS PRO GLY LEU VAL VAL GLU LEU VAL SEQRES 4 A 313 PRO MET VAL THR ARG GLY ASP VAL ILE LEU ASP THR PRO SEQRES 5 A 313 LEU ALA LYS VAL GLY GLY LYS GLY LEU PHE VAL LYS GLU SEQRES 6 A 313 LEU GLU VAL ALA LEU LEU GLU ASN ARG ALA ASP ILE ALA SEQRES 7 A 313 VAL HIS SER MET LYS ASP VAL PRO VAL GLU PHE PRO GLN SEQRES 8 A 313 GLY LEU GLY LEU VAL THR ILE CYS GLU ARG GLU ASP PRO SEQRES 9 A 313 ARG ASP ALA PHE VAL SER ASN ASN TYR ASP SER LEU ASP SEQRES 10 A 313 ALA LEU PRO ALA GLY SER ILE VAL GLY THR SER SER LEU SEQRES 11 A 313 ARG ARG GLN CYS GLN LEU ALA GLU ARG ARG PRO ASP LEU SEQRES 12 A 313 ILE ILE ARG SER LEU ARG GLY ASN VAL GLY THR ARG LEU SEQRES 13 A 313 SER LYS LEU ASP ASN GLY GLU TYR ASP ALA ILE ILE LEU SEQRES 14 A 313 ALA VAL ALA GLY LEU LYS ARG LEU GLY LEU GLU SER ARG SEQRES 15 A 313 ILE ARG ALA ALA LEU PRO PRO GLU ILE SER LEU PRO ALA SEQRES 16 A 313 VAL GLY GLN GLY ALA VAL GLY ILE GLU CYS ARG LEU ASP SEQRES 17 A 313 ASP SER ARG THR ARG GLU LEU LEU ALA ALA LEU ASN HIS SEQRES 18 A 313 HIS GLU THR ALA LEU ARG VAL THR ALA GLU ARG ALA MET SEQRES 19 A 313 ASN THR ARG LEU GLU GLY GLY CYS GLN VAL PRO ILE GLY SEQRES 20 A 313 SER TYR ALA GLU LEU ILE ASP GLY GLU ILE TRP LEU ARG SEQRES 21 A 313 ALA LEU VAL GLY ALA PRO ASP GLY SER GLN ILE ILE ARG SEQRES 22 A 313 GLY GLU ARG ARG GLY ALA PRO GLN ASP ALA GLU GLN MET SEQRES 23 A 313 GLY ILE SER LEU ALA GLU GLU LEU LEU ASN ASN GLY ALA SEQRES 24 A 313 ARG GLU ILE LEU ALA GLU VAL TYR ASN GLY ASP ALA PRO SEQRES 25 A 313 ALA HET DPM A 315 30 HETNAM DPM 3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL- HETNAM 2 DPM 1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3- HETNAM 3 DPM YL]PROPANOIC ACID HETSYN DPM DIPYRROMETHANE COFACTOR FORMUL 2 DPM C20 H24 N2 O8 FORMUL 3 HOH *320(H2 O) HELIX 1 1 SER A 13 HIS A 31 1 19 HELIX 2 2 PHE A 62 GLU A 72 1 11 HELIX 3 3 LYS A 83 VAL A 85 5 3 HELIX 4 4 SER A 115 LEU A 119 5 5 HELIX 5 5 SER A 129 ARG A 140 1 12 HELIX 6 6 ASN A 151 ASN A 161 1 11 HELIX 7 7 VAL A 171 LEU A 177 1 7 HELIX 8 8 LEU A 179 ILE A 183 5 5 HELIX 9 9 ASP A 209 ALA A 217 1 9 HELIX 10 10 ALA A 218 ASN A 220 5 3 HELIX 11 11 HIS A 221 GLU A 239 1 19 HELIX 12 12 ALA A 279 GLN A 281 5 3 HELIX 13 13 ASP A 282 ASN A 297 1 16 HELIX 14 14 GLY A 298 GLU A 305 1 8 SHEET 1 AA 5 VAL A 35 PRO A 40 0 SHEET 2 AA 5 VAL A 5 THR A 10 1 O LEU A 6 N GLU A 37 SHEET 3 AA 5 ILE A 77 SER A 81 1 O ILE A 77 N ALA A 9 SHEET 4 AA 5 VAL A 201 ARG A 206 -1 O GLY A 202 N HIS A 80 SHEET 5 AA 5 LEU A 93 ILE A 98 -1 O GLY A 94 N CYS A 205 SHEET 1 AB 5 ILE A 144 ARG A 146 0 SHEET 2 AB 5 ILE A 124 GLY A 126 1 O VAL A 125 N ARG A 146 SHEET 3 AB 5 ALA A 166 ALA A 170 1 O ALA A 166 N GLY A 126 SHEET 4 AB 5 ASP A 106 VAL A 109 -1 O ALA A 107 N LEU A 169 SHEET 5 AB 5 ALA A 185 ALA A 186 -1 O ALA A 185 N PHE A 108 SHEET 1 AC 3 ILE A 246 ILE A 253 0 SHEET 2 AC 3 GLU A 256 GLY A 264 -1 O GLU A 256 N ILE A 253 SHEET 3 AC 3 ILE A 271 GLY A 278 -1 O ILE A 272 N VAL A 263 LINK SG CYS A 242 CHA DPM A 315 1555 1555 1.87 SITE 1 AC1 21 LEU A 15 SER A 81 LYS A 83 ASP A 84 SITE 2 AC1 21 THR A 127 SER A 128 SER A 129 ARG A 131 SITE 3 AC1 21 ARG A 132 LEU A 148 ARG A 155 LEU A 169 SITE 4 AC1 21 ALA A 170 GLN A 198 GLY A 199 CYS A 242 SITE 5 AC1 21 HOH A2197 HOH A2317 HOH A2318 HOH A2319 SITE 6 AC1 21 HOH A2320 CRYST1 87.500 75.900 50.100 90.00 90.00 90.00 P 21 21 2 4 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 0.011428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019960 0.00000