HEADER TRANSFERASE/TRANSFERASE INHIBITOR 01-NOV-12 4HTG TITLE PORPHOBILINOGEN DEAMINASE FROM ARABIDOPSIS THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PBG, HYDROXYMETHYLBILANE SYNTHASE, HMBS, PRE- COMPND 5 UROPORPHYRINOGEN SYNTHASE; COMPND 6 EC: 2.5.1.61; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT5G08280, F8L15_10, HEMC; 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: T7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS TYPE-II PERIPLASMIC BINDING PROTEIN FOLD, PORPHYRIN BINDING, KEYWDS 2 TETRAPYRROLE BIOSYNTHESIS, PORPHOBILINOGEN (PORPHYRIN) BINDING, KEYWDS 3 CHLOROPLAST, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.ROBERTS,R.GILL,R.J.HUSSEY,P.T.ERSKINE,J.B.COOPER,S.P.WOOD, AUTHOR 2 E.J.T.CHRYSTAL,P.M.SHOOLINGIN-JORDAN REVDAT 3 20-SEP-23 4HTG 1 REMARK LINK REVDAT 2 03-APR-13 4HTG 1 JRNL REVDAT 1 27-FEB-13 4HTG 0 JRNL AUTH A.ROBERTS,R.GILL,R.J.HUSSEY,H.MIKOLAJEK,P.T.ERSKINE, JRNL AUTH 2 J.B.COOPER,S.P.WOOD,E.J.CHRYSTAL,P.M.SHOOLINGIN-JORDAN JRNL TITL INSIGHTS INTO THE MECHANISM OF PYRROLE POLYMERIZATION JRNL TITL 2 CATALYSED BY PORPHOBILINOGEN DEAMINASE: HIGH-RESOLUTION JRNL TITL 3 X-RAY STUDIES OF THE ARABIDOPSIS THALIANA ENZYME. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 471 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23519422 JRNL DOI 10.1107/S0907444912052134 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 46662 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2455 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3206 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 164 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2289 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 409 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.992 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2405 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3254 ; 2.052 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 311 ; 5.763 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;36.967 ;24.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;15.465 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.794 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 378 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1774 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 2405 ; 6.360 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 149 ;38.308 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2627 ;19.639 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 110 REMARK 3 RESIDUE RANGE : A 212 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): -39.6133 -7.0468 14.1149 REMARK 3 T TENSOR REMARK 3 T11: 0.0022 T22: 0.0218 REMARK 3 T33: 0.0049 T12: -0.0002 REMARK 3 T13: -0.0011 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0060 L22: 0.0020 REMARK 3 L33: 0.0069 L12: -0.0014 REMARK 3 L13: -0.0044 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: 0.0002 S13: 0.0007 REMARK 3 S21: -0.0004 S22: -0.0001 S23: 0.0002 REMARK 3 S31: -0.0003 S32: 0.0021 S33: -0.0008 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 111 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): -22.0566 -0.8627 31.9124 REMARK 3 T TENSOR REMARK 3 T11: 0.0017 T22: 0.0222 REMARK 3 T33: 0.0048 T12: 0.0002 REMARK 3 T13: -0.0008 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0207 L22: 0.0149 REMARK 3 L33: 0.0185 L12: -0.0116 REMARK 3 L13: 0.0141 L23: -0.0121 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: -0.0033 S13: 0.0021 REMARK 3 S21: -0.0011 S22: 0.0020 S23: -0.0013 REMARK 3 S31: -0.0022 S32: -0.0009 S33: -0.0002 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 230 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): -16.8653 -13.6912 15.0597 REMARK 3 T TENSOR REMARK 3 T11: 0.0023 T22: 0.0224 REMARK 3 T33: 0.0045 T12: 0.0001 REMARK 3 T13: -0.0008 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0099 L22: 0.0002 REMARK 3 L33: 0.0066 L12: 0.0012 REMARK 3 L13: 0.0074 L23: 0.0006 REMARK 3 S TENSOR REMARK 3 S11: 0.0003 S12: 0.0009 S13: 0.0027 REMARK 3 S21: 0.0003 S22: -0.0005 S23: 0.0007 REMARK 3 S31: 0.0003 S32: 0.0027 S33: 0.0001 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: REFMAC USING RIDING HYDROGENS, REMARK 3 ANISOTROPIC B-FACTORS AND EACH OF THE THREE PROTEIN DOMAINS AS A REMARK 3 SEPARATE TLS GROUP. REMARK 4 REMARK 4 4HTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 32.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.76700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 39.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MG/ML PROTEIN ADDED IN 50:50 RATIO REMARK 280 TO THE WELL-SOLUTION OF 25% PEG 4000, 100 MM SODIUM CITRATE, 200 REMARK 280 MM AMMONIUM SULPHATE. CRYSTALS GROWN IN THE DARK DUE TO REMARK 280 PHOTOSENSITIVITY OF THE COFACTOR., PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 70.78650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.63550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.78650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.63550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 -1.000000 0.000000 0.000000 -14.25291 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.19257 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 CYS A 1 REMARK 465 VAL A 2 REMARK 465 ALA A 3 REMARK 465 VAL A 4 REMARK 465 GLU A 5 REMARK 465 GLN A 6 REMARK 465 LYS A 7 REMARK 465 THR A 8 REMARK 465 ARG A 9 REMARK 465 ARG A 312 REMARK 465 ALA A 313 REMARK 465 GLY A 314 REMARK 465 PRO A 315 REMARK 465 GLY A 316 REMARK 465 PHE A 317 REMARK 465 PHE A 318 REMARK 465 GLY A 319 REMARK 465 ASN A 320 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 510 O HOH A 813 2.05 REMARK 500 O HOH A 636 O HOH A 836 2.14 REMARK 500 OD2 ASP A 78 O HOH A 701 2.19 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 HIS A 38 CG HIS A 38 CD2 0.064 REMARK 500 HIS A 48 CG HIS A 48 CD2 0.054 REMARK 500 HIS A 233 CG HIS A 233 CD2 0.056 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 LEU A 64 CB - CG - CD2 ANGL. DEV. = -12.1 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 LYS A 103 3.59 84.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 18W A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PDA RELATED DB: PDB REMARK 900 PORPHOBILINOGEN DEAMINASE FROM E. COLI REMARK 900 RELATED ID: 1GTK RELATED DB: PDB REMARK 900 PORPHOBILINOGEN DEAMINASE FROM E. COLI REMARK 900 RELATED ID: 3EQ1 RELATED DB: PDB REMARK 900 PORPHOBILINOGEN DEAMINASE FROM H. SAPIENS REMARK 900 RELATED ID: 3ECR RELATED DB: PDB REMARK 900 PORPHOBILINOGEN DEAMINASE FROM H. SAPIENS DBREF 4HTG A 1 320 UNP Q43316 HEM3_ARATH 63 382 SEQRES 1 A 320 CYS VAL ALA VAL GLU GLN LYS THR ARG THR ALA ILE ILE SEQRES 2 A 320 ARG ILE GLY THR ARG GLY SER PRO LEU ALA LEU ALA GLN SEQRES 3 A 320 ALA TYR GLU THR ARG GLU LYS LEU LYS LYS LYS HIS PRO SEQRES 4 A 320 GLU LEU VAL GLU ASP GLY ALA ILE HIS ILE GLU ILE ILE SEQRES 5 A 320 LYS THR THR GLY ASP LYS ILE LEU SER GLN PRO LEU ALA SEQRES 6 A 320 ASP ILE GLY GLY LYS GLY LEU PHE THR LYS GLU ILE ASP SEQRES 7 A 320 GLU ALA LEU ILE ASN GLY HIS ILE ASP ILE ALA VAL HIS SEQRES 8 A 320 SER MET LYS ASP VAL PRO THR TYR LEU PRO GLU LYS THR SEQRES 9 A 320 ILE LEU PRO CYS ASN LEU PRO ARG GLU ASP VAL ARG ASP SEQRES 10 A 320 ALA PHE ILE CYS LEU THR ALA ALA THR LEU ALA GLU LEU SEQRES 11 A 320 PRO ALA GLY SER VAL VAL GLY THR ALA SER LEU ARG ARG SEQRES 12 A 320 LYS SER GLN ILE LEU HIS LYS TYR PRO ALA LEU HIS VAL SEQRES 13 A 320 GLU GLU ASN PHE ARG GLY ASN VAL GLN THR ARG LEU SER SEQRES 14 A 320 LYS LEU GLN GLY GLY LYS VAL GLN ALA THR LEU LEU ALA SEQRES 15 A 320 LEU ALA GLY LEU LYS ARG LEU SER MET THR GLU ASN VAL SEQRES 16 A 320 ALA SER ILE LEU SER LEU ASP GLU MET LEU PRO ALA VAL SEQRES 17 A 320 ALA GLN GLY ALA ILE GLY ILE ALA CYS ARG THR ASP ASP SEQRES 18 A 320 ASP LYS MET ALA THR TYR LEU ALA SER LEU ASN HIS GLU SEQRES 19 A 320 GLU THR ARG LEU ALA ILE SER CYS GLU ARG ALA PHE LEU SEQRES 20 A 320 GLU THR LEU ASP GLY SER CYS ARG THR PRO ILE ALA GLY SEQRES 21 A 320 TYR ALA SER LYS ASP GLU GLU GLY ASN CYS ILE PHE ARG SEQRES 22 A 320 GLY LEU VAL ALA SER PRO ASP GLY THR LYS VAL LEU GLU SEQRES 23 A 320 THR SER ARG LYS GLY PRO TYR VAL TYR GLU ASP MET VAL SEQRES 24 A 320 LYS MET GLY LYS ASP ALA GLY GLN GLU LEU LEU SER ARG SEQRES 25 A 320 ALA GLY PRO GLY PHE PHE GLY ASN HET 18W A 401 31 HET ACT A 402 4 HETNAM 18W 3-[(5Z)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5- HETNAM 2 18W METHYL-1H-PYRROL-2-YL]METHYLIDENE}-4-(CARBOXYMETHYL)- HETNAM 3 18W 2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID HETNAM ACT ACETATE ION FORMUL 2 18W C20 H22 N2 O9 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *409(H2 O) HELIX 1 1 SER A 20 HIS A 38 1 19 HELIX 2 2 PRO A 39 VAL A 42 5 4 HELIX 3 3 THR A 54 LYS A 58 5 5 HELIX 4 4 PRO A 63 ILE A 67 5 5 HELIX 5 5 THR A 74 ASN A 83 1 10 HELIX 6 6 LYS A 94 VAL A 96 5 3 HELIX 7 7 THR A 126 LEU A 130 5 5 HELIX 8 8 SER A 140 TYR A 151 1 12 HELIX 9 9 ASN A 163 GLY A 173 1 11 HELIX 10 10 LEU A 183 SER A 190 1 8 HELIX 11 11 MET A 191 VAL A 195 5 5 HELIX 12 12 ASP A 221 SER A 230 1 10 HELIX 13 13 HIS A 233 LEU A 250 1 18 HELIX 14 14 VAL A 294 SER A 311 1 18 SHEET 1 A 5 ILE A 47 ILE A 51 0 SHEET 2 A 5 ILE A 13 THR A 17 1 N ILE A 15 O HIS A 48 SHEET 3 A 5 ILE A 88 SER A 92 1 O ILE A 88 N GLY A 16 SHEET 4 A 5 ILE A 213 ARG A 218 -1 O GLY A 214 N HIS A 91 SHEET 5 A 5 THR A 104 ASN A 109 -1 N ILE A 105 O CYS A 217 SHEET 1 B 5 HIS A 155 GLU A 157 0 SHEET 2 B 5 VAL A 135 GLY A 137 1 N VAL A 136 O HIS A 155 SHEET 3 B 5 ALA A 178 ALA A 182 1 O ALA A 178 N GLY A 137 SHEET 4 B 5 ASP A 117 CYS A 121 -1 N ALA A 118 O LEU A 181 SHEET 5 B 5 SER A 197 ILE A 198 -1 O SER A 197 N PHE A 119 SHEET 1 C 3 ILE A 258 LYS A 264 0 SHEET 2 C 3 ASN A 269 ALA A 277 -1 O ILE A 271 N SER A 263 SHEET 3 C 3 VAL A 284 PRO A 292 -1 O GLY A 291 N CYS A 270 LINK SG CYS A 254 CHA 18W A 401 1555 1555 1.96 SITE 1 AC1 22 ARG A 18 SER A 20 LEU A 64 PHE A 73 SITE 2 AC1 22 LYS A 94 ASP A 95 THR A 138 ALA A 139 SITE 3 AC1 22 SER A 140 ARG A 142 ARG A 143 ARG A 161 SITE 4 AC1 22 GLY A 162 ASN A 163 VAL A 164 ARG A 167 SITE 5 AC1 22 ALA A 207 CYS A 254 HOH A 514 HOH A 651 SITE 6 AC1 22 HOH A 782 HOH A 881 SITE 1 AC2 6 LYS A 94 ARG A 143 LEU A 181 ALA A 182 SITE 2 AC2 6 HOH A 517 HOH A 728 CRYST1 141.573 37.271 55.069 90.00 105.00 90.00 C 1 2 1 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 0.007063 0.000000 0.001892 0.00000 SCALE2 0.000000 0.026830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018800 0.00000