HEADER TRANSFERASE 06-SEP-13 4MLV TITLE CRYSTAL STRUCTURE OF BACILLUS MEGATERIUM PORPHOBILINOGEN DEAMINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PORPHOBILINOGEN DEAMINASE; COMPND 5 SYNONYM: PBG, HYDROXYMETHYLBILANE SYNTHASE, PRE-UROPORPHYRINOGEN COMPND 6 SYNTHASE; COMPND 7 EC: 2.5.1.61; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 GENE: HEMC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS TETRAPYRROLE BIOSYNTHESIS, PORPHOBILINOGEN DEAMINASE, DIPYRROMETHANE KEYWDS 2 COFACTOR, THREE-DOMAIN FOLD, DOMAINS 1 AND 2 RESEMBLE THE FOLD OF KEYWDS 3 TYPE II PERIPLASMIC BINDING PROTEINS, PYRROLE POLYMERISATION, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.AZIM,E.DEERY,M.J.WARREN,P.ERSKINE,J.B.COOPER,A.COKER,S.P.WOOD, AUTHOR 2 M.AKHTAR REVDAT 1 02-APR-14 4MLV 0 JRNL AUTH N.AZIM,E.DEERY,M.J.WARREN,B.A.WOLFENDEN,P.ERSKINE, JRNL AUTH 2 J.B.COOPER,A.COKER,S.P.WOOD,M.AKHTAR JRNL TITL STRUCTURAL EVIDENCE FOR THE PARTIALLY OXIDIZED JRNL TITL 2 DIPYRROMETHENE AND DIPYRROMETHANONE FORMS OF THE COFACTOR OF JRNL TITL 3 PORPHOBILINOGEN DEAMINASE: STRUCTURES OF THE BACILLUS JRNL TITL 4 MEGATERIUM ENZYME AT NEAR-ATOMIC RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 744 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24598743 JRNL DOI 10.1107/S139900471303294X REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57626 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3073 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) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4176 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 249 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.028 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2366 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2331 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3180 ; 2.438 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5403 ; 2.208 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 288 ; 6.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;37.127 ;24.608 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 460 ;13.854 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;22.985 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2613 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 469 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1159 ; 2.796 ; 1.950 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1157 ; 2.734 ; 1.943 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1444 ; 3.325 ; 2.919 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1445 ; 3.331 ; 2.926 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1207 ; 5.685 ; 2.522 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1205 ; 5.689 ; 2.524 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1736 ; 5.589 ; 3.579 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2810 ; 4.980 ;17.597 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2690 ; 4.808 ;16.882 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4697 ; 8.154 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 114 ;25.619 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4879 ;11.816 ; 5.000 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 4MLV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-13. REMARK 100 THE RCSB ID CODE IS RCSB082073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 - 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.455 REMARK 200 RESOLUTION RANGE LOW (A) : 48.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.55900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 1PDA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CACODYLATE, 0.2M MAGNESIUM REMARK 280 ACETATE, 25-30% PEG 8K, PH 6.5 - 6.8, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298.0K 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 26.66000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.60500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.60500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.66000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.89000 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 VAL A 40 REMARK 465 THR A 41 REMARK 465 LYS A 42 REMARK 465 GLY A 43 REMARK 465 ASP A 44 REMARK 465 GLN A 45 REMARK 465 ILE A 46 REMARK 465 LEU A 47 REMARK 465 ASN A 48 REMARK 465 VAL A 49 REMARK 465 THR A 50 REMARK 465 LEU A 51 REMARK 465 SER A 52 REMARK 465 LYS A 53 REMARK 465 VAL A 54 REMARK 465 GLY A 55 REMARK 465 GLY A 56 REMARK 465 LYS A 57 REMARK 465 GLY A 58 REMARK 465 LEU A 59 REMARK 465 PHE A 60 REMARK 465 LYS A 310 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 HOH A 568 O HOH A 641 2.18 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 GLU A 116 CD GLU A 116 OE1 0.090 REMARK 500 ARG A 174 CZ ARG A 174 NH2 -0.087 REMARK 500 GLU A 222 CG GLU A 222 CD 0.096 REMARK 500 VAL A 243 CA VAL A 243 CB 0.128 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 82 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ILE A 150 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 174 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLU A 222 CA - CB - CG ANGL. DEV. = 23.5 DEGREES REMARK 500 ASP A 280 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 LEU A 292 CB - CG - CD2 ANGL. DEV. = 11.3 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 ASP A 140 35.98 -91.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 190 22.8 L L OUTSIDE RANGE 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 A 634 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A 642 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 646 DISTANCE = 9.24 ANGSTROMS REMARK 525 HOH A 647 DISTANCE = 11.38 ANGSTROMS REMARK 525 HOH A 652 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 671 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH A 672 DISTANCE = 10.71 ANGSTROMS REMARK 525 HOH A 687 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A 700 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A 705 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH A 709 DISTANCE = 8.16 ANGSTROMS REMARK 525 HOH A 711 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH A 721 DISTANCE = 5.61 ANGSTROMS REMARK 525 HOH A 722 DISTANCE = 9.00 ANGSTROMS REMARK 525 HOH A 723 DISTANCE = 10.93 ANGSTROMS REMARK 525 HOH A 726 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A 733 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 742 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 747 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH A 756 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 757 DISTANCE = 7.27 ANGSTROMS REMARK 525 HOH A 758 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH A 773 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH A 782 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 793 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A 798 DISTANCE = 5.02 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 29P A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PDA RELATED DB: PDB REMARK 900 STRUCTURE OF ESCHERICHIA COLI PORPHOBILINOGEN DEAMINASE REMARK 900 RELATED ID: 4HTG RELATED DB: PDB REMARK 900 STRUCTURE OF ARABIDOPSIS THALIANA PORPHOBILINOGEN DEAMINASE DBREF 4MLV A 1 310 UNP Q8GCA8 Q8GCA8_BACME 1 310 SEQADV 4MLV SER A -1 UNP Q8GCA8 EXPRESSION TAG SEQADV 4MLV HIS A 0 UNP Q8GCA8 EXPRESSION TAG SEQRES 1 A 312 SER HIS MET ARG LYS ILE ILE VAL GLY SER ARG ARG SER SEQRES 2 A 312 LYS LEU ALA LEU THR GLN THR LYS TRP VAL ILE GLU GLN SEQRES 3 A 312 LEU LYS LYS GLN GLY LEU PRO PHE GLU PHE GLU ILE LYS SEQRES 4 A 312 GLU MET VAL THR LYS GLY ASP GLN ILE LEU ASN VAL THR SEQRES 5 A 312 LEU SER LYS VAL GLY GLY LYS GLY LEU PHE VAL LYS GLU SEQRES 6 A 312 ILE GLU GLN ALA MET LEU ASP LYS GLU ILE ASP MET ALA SEQRES 7 A 312 VAL HIS SER MET LYS ASP MET PRO ALA VAL LEU PRO GLU SEQRES 8 A 312 GLY LEU THR ILE GLY CYS ILE PRO LEU ARG GLU ASP HIS SEQRES 9 A 312 ARG ASP ALA LEU ILE SER LYS ASN GLY GLU ARG PHE GLU SEQRES 10 A 312 GLU LEU PRO SER GLY ALA VAL ILE GLY THR SER SER LEU SEQRES 11 A 312 ARG ARG GLY ALA GLN LEU LEU SER MET ARG SER ASP ILE SEQRES 12 A 312 GLU ILE LYS TRP ILE ARG GLY ASN ILE ASP THR ARG LEU SEQRES 13 A 312 GLU LYS LEU LYS ASN GLU ASP TYR ASP ALA ILE ILE LEU SEQRES 14 A 312 ALA ALA ALA GLY LEU SER ARG MET GLY TRP SER LYS ASP SEQRES 15 A 312 THR VAL THR GLN TYR LEU GLU PRO GLU ILE SER VAL PRO SEQRES 16 A 312 ALA VAL GLY GLN GLY ALA LEU ALA ILE GLU CYS ARG GLU SEQRES 17 A 312 ASN ASP HIS GLU LEU LEU SER LEU LEU GLN ALA LEU ASN SEQRES 18 A 312 HIS ASP GLU THR ALA ARG ALA VAL ARG ALA GLU ARG VAL SEQRES 19 A 312 PHE LEU LYS GLU MET GLU GLY GLY CYS GLN VAL PRO ILE SEQRES 20 A 312 ALA GLY TYR GLY ARG ILE LEU ASP GLY GLY ASN ILE GLU SEQRES 21 A 312 LEU THR SER LEU VAL ALA SER PRO ASP GLY LYS THR ILE SEQRES 22 A 312 TYR LYS GLU HIS ILE THR GLY LYS ASP PRO ILE ALA ILE SEQRES 23 A 312 GLY SER GLU ALA ALA GLU ARG LEU THR SER GLN GLY ALA SEQRES 24 A 312 LYS LEU LEU ILE ASP ARG VAL LYS GLU GLU LEU ASP LYS HET DPM A 401 30 HET 29P A 402 31 HET ACY A 403 4 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 HETNAM 29P 3-[(5S)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5- HETNAM 2 29P METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-2-OXO- HETNAM 3 29P 2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID HETNAM ACY ACETIC ACID HETSYN DPM DIPYRROMETHANE COFACTOR HETSYN 29P DIPYRROMETHANONE FORMUL 2 DPM C20 H24 N2 O8 FORMUL 3 29P C20 H24 N2 O9 FORMUL 4 ACY C2 H4 O2 FORMUL 5 HOH *325(H2 O) HELIX 1 1 SER A 11 LYS A 27 1 17 HELIX 2 2 LYS A 62 ASP A 70 1 9 HELIX 3 3 LYS A 81 MET A 83 5 3 HELIX 4 4 ARG A 113 LEU A 117 5 5 HELIX 5 5 SER A 127 ARG A 138 1 12 HELIX 6 6 ASN A 149 GLU A 160 1 12 HELIX 7 7 ALA A 169 MET A 175 1 7 HELIX 8 8 ASP A 208 ALA A 217 1 10 HELIX 9 9 HIS A 220 MET A 237 1 18 HELIX 10 10 ASP A 280 GLY A 296 1 17 HELIX 11 11 GLY A 296 GLU A 307 1 12 SHEET 1 A 5 PHE A 32 GLU A 38 0 SHEET 2 A 5 ARG A 2 SER A 8 1 N ILE A 4 O GLU A 33 SHEET 3 A 5 MET A 75 SER A 79 1 O MET A 75 N GLY A 7 SHEET 4 A 5 LEU A 200 ARG A 205 -1 O ALA A 201 N HIS A 78 SHEET 5 A 5 LEU A 91 CYS A 95 -1 N THR A 92 O CYS A 204 SHEET 1 B 5 ILE A 141 LYS A 144 0 SHEET 2 B 5 ALA A 121 GLY A 124 1 N ILE A 123 O GLU A 142 SHEET 3 B 5 ALA A 164 ALA A 168 1 O ALA A 164 N GLY A 124 SHEET 4 B 5 ASP A 104 SER A 108 -1 N ALA A 105 O LEU A 167 SHEET 5 B 5 GLN A 184 TYR A 185 -1 O GLN A 184 N LEU A 106 SHEET 1 C 3 ILE A 245 ILE A 251 0 SHEET 2 C 3 ILE A 257 ALA A 264 -1 O THR A 260 N TYR A 248 SHEET 3 C 3 ILE A 271 GLY A 278 -1 O TYR A 272 N VAL A 263 LINK SG CYS A 241 CHAADPM A 401 1555 1555 1.82 LINK SG CYS A 241 CHAB29P A 402 1555 1555 1.83 SITE 1 AC1 18 SER A 79 LYS A 81 ASP A 82 THR A 125 SITE 2 AC1 18 SER A 126 SER A 127 ARG A 129 ARG A 130 SITE 3 AC1 18 ARG A 153 ALA A 168 ALA A 194 GLN A 197 SITE 4 AC1 18 GLY A 198 CYS A 241 HOH A 506 HOH A 544 SITE 5 AC1 18 HOH A 559 HOH A 565 SITE 1 AC2 19 ARG A 9 SER A 11 LEU A 13 LYS A 81 SITE 2 AC2 19 ASP A 82 THR A 125 SER A 126 SER A 127 SITE 3 AC2 19 ARG A 129 ARG A 130 ARG A 147 GLY A 148 SITE 4 AC2 19 ASN A 149 ILE A 150 ARG A 153 ALA A 194 SITE 5 AC2 19 CYS A 241 HOH A 618 HOH A 801 SITE 1 AC3 5 PHE A 34 GLU A 35 ILE A 36 ARG A 303 SITE 2 AC3 5 HOH A 790 CRYST1 53.320 65.780 97.210 90.00 90.00 90.00 P 21 21 21 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 0.018755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010287 0.00000 MASTER 416 0 3 11 13 0 12 6 0 0 0 24 END