HEADER TRANSFERASE 27-OCT-16 5M7F TITLE HUMAN PORPHOBILINOGEN DEAMINASE IN COMPLEX WITH DPM COFACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PBG-D,HYDROXYMETHYLBILANE SYNTHASE,HMBS,PRE-UROPORPHYRINOGEN COMPND 5 SYNTHASE; COMPND 6 EC: 2.5.1.61; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HMBS, PBGD, UPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORPHOBILINOGEN DEAMINASE, HEME BIOSYNTHESIS, PORPHYRIA, HMBS, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PLUTA,O.MILLET,P.ROVERSI,A.L.ROJAS,S.GU REVDAT 3 17-JAN-24 5M7F 1 REMARK REVDAT 2 29-MAY-19 5M7F 1 JRNL REVDAT 1 15-NOV-17 5M7F 0 JRNL AUTH P.PLUTA,P.ROVERSI,G.BERNARDO-SEISDEDOS,A.L.ROJAS,J.B.COOPER, JRNL AUTH 2 S.GU,R.W.PICKERSGILL,O.MILLET JRNL TITL STRUCTURAL BASIS OF PYRROLE POLYMERIZATION IN HUMAN JRNL TITL 2 PORPHOBILINOGEN DEAMINASE. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1862 1948 2018 JRNL REF 2 SUBJ JRNL REFN ISSN 0304-4165 JRNL PMID 29908816 JRNL DOI 10.1016/J.BBAGEN.2018.06.013 REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 21279 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1112 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.77 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2621 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2520 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2509 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.27 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 112 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4878 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.34830 REMARK 3 B22 (A**2) : 21.04900 REMARK 3 B33 (A**2) : -14.70080 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -19.36860 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.460 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.986 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.340 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.856 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.848 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 10067 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 18272 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2250 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 126 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1533 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 10067 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 653 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 11301 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.23 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.40 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 1.4876 -0.8700 24.3874 REMARK 3 T TENSOR REMARK 3 T11: 0.0067 T22: -0.0997 REMARK 3 T33: -0.0069 T12: 0.0834 REMARK 3 T13: 0.1916 T23: 0.0284 REMARK 3 L TENSOR REMARK 3 L11: 1.4368 L22: 2.2999 REMARK 3 L33: 2.2895 L12: 0.4354 REMARK 3 L13: -1.1094 L23: -0.0527 REMARK 3 S TENSOR REMARK 3 S11: 0.1441 S12: 0.1125 S13: 0.1469 REMARK 3 S21: 0.0989 S22: 0.0290 S23: 0.1859 REMARK 3 S31: -0.2125 S32: -0.1479 S33: -0.1731 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -20.9142 14.2536 -2.4437 REMARK 3 T TENSOR REMARK 3 T11: -0.0630 T22: -0.0555 REMARK 3 T33: 0.0284 T12: 0.0006 REMARK 3 T13: 0.1441 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 1.7654 L22: 3.7019 REMARK 3 L33: 1.5846 L12: 0.3031 REMARK 3 L13: -1.0007 L23: -0.0875 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: -0.0929 S13: -0.2129 REMARK 3 S21: -0.0383 S22: 0.0599 S23: -0.3085 REMARK 3 S31: -0.0739 S32: 0.1607 S33: 0.0164 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200002058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972422 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION MAY 1, 2016 REMARK 200 DATA SCALING SOFTWARE : AIMLESS VERSION 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21353 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 80.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.24700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 1.26500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 3ECR REMARK 200 REMARK 200 REMARK: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M REMARK 280 SODIUM CHLORIDE, 2 M AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.47500 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 -3 REMARK 465 GLY A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 SER A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 HIS A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 REMARK 465 GLY A 15 REMARK 465 ARG A 16 REMARK 465 HIS A 17 REMARK 465 MET A 18 REMARK 465 ARG A 19 REMARK 465 THR A 58 REMARK 465 THR A 59 REMARK 465 GLY A 60 REMARK 465 ASP A 61 REMARK 465 LYS A 62 REMARK 465 ILE A 63 REMARK 465 LEU A 64 REMARK 465 ASP A 65 REMARK 465 THR A 66 REMARK 465 ALA A 67 REMARK 465 LEU A 68 REMARK 465 SER A 69 REMARK 465 LYS A 70 REMARK 465 ILE A 71 REMARK 465 GLY A 72 REMARK 465 GLU A 73 REMARK 465 LYS A 74 REMARK 465 ALA A 354 REMARK 465 ARG A 355 REMARK 465 GLN A 356 REMARK 465 LEU A 357 REMARK 465 ASN A 358 REMARK 465 ASP A 359 REMARK 465 ALA A 360 REMARK 465 HIS A 361 REMARK 465 MET B -3 REMARK 465 GLY B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 HIS B 2 REMARK 465 HIS B 3 REMARK 465 HIS B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 SER B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 HIS B 12 REMARK 465 ILE B 13 REMARK 465 GLU B 14 REMARK 465 GLY B 15 REMARK 465 ARG B 16 REMARK 465 HIS B 17 REMARK 465 MET B 18 REMARK 465 ARG B 19 REMARK 465 SER B 57 REMARK 465 THR B 58 REMARK 465 THR B 59 REMARK 465 GLY B 60 REMARK 465 ASP B 61 REMARK 465 LYS B 62 REMARK 465 ILE B 63 REMARK 465 LEU B 64 REMARK 465 ASP B 65 REMARK 465 THR B 66 REMARK 465 ALA B 67 REMARK 465 LEU B 68 REMARK 465 SER B 69 REMARK 465 LYS B 70 REMARK 465 ILE B 71 REMARK 465 GLY B 72 REMARK 465 GLU B 73 REMARK 465 LYS B 74 REMARK 465 ALA B 354 REMARK 465 ARG B 355 REMARK 465 GLN B 356 REMARK 465 LEU B 357 REMARK 465 ASN B 358 REMARK 465 ASP B 359 REMARK 465 ALA B 360 REMARK 465 HIS B 361 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 GLU A 210 -67.79 -91.71 REMARK 500 GLU A 258 38.49 71.22 REMARK 500 SER A 262 57.68 -92.37 REMARK 500 TRP B 198 45.47 -88.19 REMARK 500 GLU B 210 -69.27 -92.07 REMARK 500 GLU B 258 37.85 70.40 REMARK 500 SER B 262 57.49 -92.65 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 DPM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DPM B 401 and CYS B REMARK 800 261 DBREF 5M7F A 18 361 UNP P08397 HEM3_HUMAN 1 344 DBREF 5M7F B 18 361 UNP P08397 HEM3_HUMAN 1 344 SEQADV 5M7F MET A -3 UNP P08397 INITIATING METHIONINE SEQADV 5M7F GLY A -2 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A -1 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 0 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 1 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 2 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 3 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 4 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 5 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 6 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 7 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 8 UNP P08397 EXPRESSION TAG SEQADV 5M7F SER A 9 UNP P08397 EXPRESSION TAG SEQADV 5M7F SER A 10 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLY A 11 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 12 UNP P08397 EXPRESSION TAG SEQADV 5M7F ILE A 13 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLU A 14 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLY A 15 UNP P08397 EXPRESSION TAG SEQADV 5M7F ARG A 16 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS A 17 UNP P08397 EXPRESSION TAG SEQADV 5M7F MET B -3 UNP P08397 INITIATING METHIONINE SEQADV 5M7F GLY B -2 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B -1 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 0 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 1 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 2 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 3 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 4 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 5 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 6 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 7 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 8 UNP P08397 EXPRESSION TAG SEQADV 5M7F SER B 9 UNP P08397 EXPRESSION TAG SEQADV 5M7F SER B 10 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLY B 11 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 12 UNP P08397 EXPRESSION TAG SEQADV 5M7F ILE B 13 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLU B 14 UNP P08397 EXPRESSION TAG SEQADV 5M7F GLY B 15 UNP P08397 EXPRESSION TAG SEQADV 5M7F ARG B 16 UNP P08397 EXPRESSION TAG SEQADV 5M7F HIS B 17 UNP P08397 EXPRESSION TAG SEQRES 1 A 365 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 365 SER GLY HIS ILE GLU GLY ARG HIS MET ARG VAL ILE ARG SEQRES 3 A 365 VAL GLY THR ARG LYS SER GLN LEU ALA ARG ILE GLN THR SEQRES 4 A 365 ASP SER VAL VAL ALA THR LEU LYS ALA SER TYR PRO GLY SEQRES 5 A 365 LEU GLN PHE GLU ILE ILE ALA MET SER THR THR GLY ASP SEQRES 6 A 365 LYS ILE LEU ASP THR ALA LEU SER LYS ILE GLY GLU LYS SEQRES 7 A 365 SER LEU PHE THR LYS GLU LEU GLU HIS ALA LEU GLU LYS SEQRES 8 A 365 ASN GLU VAL ASP LEU VAL VAL HIS SER LEU LYS ASP LEU SEQRES 9 A 365 PRO THR VAL LEU PRO PRO GLY PHE THR ILE GLY ALA ILE SEQRES 10 A 365 CYS LYS ARG GLU ASN PRO HIS ASP ALA VAL VAL PHE HIS SEQRES 11 A 365 PRO LYS PHE VAL GLY LYS THR LEU GLU THR LEU PRO GLU SEQRES 12 A 365 LYS SER VAL VAL GLY THR SER SER LEU ARG ARG ALA ALA SEQRES 13 A 365 GLN LEU GLN ARG LYS PHE PRO HIS LEU GLU PHE ARG SER SEQRES 14 A 365 ILE ARG GLY ASN LEU ASN THR ARG LEU ARG LYS LEU ASP SEQRES 15 A 365 GLU GLN GLN GLU PHE SER ALA ILE ILE LEU ALA THR ALA SEQRES 16 A 365 GLY LEU GLN ARG MET GLY TRP HIS ASN ARG VAL GLY GLN SEQRES 17 A 365 ILE LEU HIS PRO GLU GLU CYS MET TYR ALA VAL GLY GLN SEQRES 18 A 365 GLY ALA LEU GLY VAL GLU VAL ARG ALA LYS ASP GLN ASP SEQRES 19 A 365 ILE LEU ASP LEU VAL GLY VAL LEU HIS ASP PRO GLU THR SEQRES 20 A 365 LEU LEU ARG CYS ILE ALA GLU ARG ALA PHE LEU ARG HIS SEQRES 21 A 365 LEU GLU GLY GLY CYS SER VAL PRO VAL ALA VAL HIS THR SEQRES 22 A 365 ALA MET LYS ASP GLY GLN LEU TYR LEU THR GLY GLY VAL SEQRES 23 A 365 TRP SER LEU ASP GLY SER ASP SER ILE GLN GLU THR MET SEQRES 24 A 365 GLN ALA THR ILE HIS VAL PRO ALA GLN HIS GLU ASP GLY SEQRES 25 A 365 PRO GLU ASP ASP PRO GLN LEU VAL GLY ILE THR ALA ARG SEQRES 26 A 365 ASN ILE PRO ARG GLY PRO GLN LEU ALA ALA GLN ASN LEU SEQRES 27 A 365 GLY ILE SER LEU ALA ASN LEU LEU LEU SER LYS GLY ALA SEQRES 28 A 365 LYS ASN ILE LEU ASP VAL ALA ARG GLN LEU ASN ASP ALA SEQRES 29 A 365 HIS SEQRES 1 B 365 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 B 365 SER GLY HIS ILE GLU GLY ARG HIS MET ARG VAL ILE ARG SEQRES 3 B 365 VAL GLY THR ARG LYS SER GLN LEU ALA ARG ILE GLN THR SEQRES 4 B 365 ASP SER VAL VAL ALA THR LEU LYS ALA SER TYR PRO GLY SEQRES 5 B 365 LEU GLN PHE GLU ILE ILE ALA MET SER THR THR GLY ASP SEQRES 6 B 365 LYS ILE LEU ASP THR ALA LEU SER LYS ILE GLY GLU LYS SEQRES 7 B 365 SER LEU PHE THR LYS GLU LEU GLU HIS ALA LEU GLU LYS SEQRES 8 B 365 ASN GLU VAL ASP LEU VAL VAL HIS SER LEU LYS ASP LEU SEQRES 9 B 365 PRO THR VAL LEU PRO PRO GLY PHE THR ILE GLY ALA ILE SEQRES 10 B 365 CYS LYS ARG GLU ASN PRO HIS ASP ALA VAL VAL PHE HIS SEQRES 11 B 365 PRO LYS PHE VAL GLY LYS THR LEU GLU THR LEU PRO GLU SEQRES 12 B 365 LYS SER VAL VAL GLY THR SER SER LEU ARG ARG ALA ALA SEQRES 13 B 365 GLN LEU GLN ARG LYS PHE PRO HIS LEU GLU PHE ARG SER SEQRES 14 B 365 ILE ARG GLY ASN LEU ASN THR ARG LEU ARG LYS LEU ASP SEQRES 15 B 365 GLU GLN GLN GLU PHE SER ALA ILE ILE LEU ALA THR ALA SEQRES 16 B 365 GLY LEU GLN ARG MET GLY TRP HIS ASN ARG VAL GLY GLN SEQRES 17 B 365 ILE LEU HIS PRO GLU GLU CYS MET TYR ALA VAL GLY GLN SEQRES 18 B 365 GLY ALA LEU GLY VAL GLU VAL ARG ALA LYS ASP GLN ASP SEQRES 19 B 365 ILE LEU ASP LEU VAL GLY VAL LEU HIS ASP PRO GLU THR SEQRES 20 B 365 LEU LEU ARG CYS ILE ALA GLU ARG ALA PHE LEU ARG HIS SEQRES 21 B 365 LEU GLU GLY GLY CYS SER VAL PRO VAL ALA VAL HIS THR SEQRES 22 B 365 ALA MET LYS ASP GLY GLN LEU TYR LEU THR GLY GLY VAL SEQRES 23 B 365 TRP SER LEU ASP GLY SER ASP SER ILE GLN GLU THR MET SEQRES 24 B 365 GLN ALA THR ILE HIS VAL PRO ALA GLN HIS GLU ASP GLY SEQRES 25 B 365 PRO GLU ASP ASP PRO GLN LEU VAL GLY ILE THR ALA ARG SEQRES 26 B 365 ASN ILE PRO ARG GLY PRO GLN LEU ALA ALA GLN ASN LEU SEQRES 27 B 365 GLY ILE SER LEU ALA ASN LEU LEU LEU SER LYS GLY ALA SEQRES 28 B 365 LYS ASN ILE LEU ASP VAL ALA ARG GLN LEU ASN ASP ALA SEQRES 29 B 365 HIS HET DPM A 401 53 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET DPM B 401 53 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 404 5 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 SO4 SULFATE ION HETSYN DPM DIPYRROMETHANE COFACTOR FORMUL 3 DPM 2(C20 H24 N2 O8) FORMUL 4 SO4 6(O4 S 2-) FORMUL 11 HOH *49(H2 O) HELIX 1 AA1 SER A 28 TYR A 46 1 19 HELIX 2 AA2 LEU A 76 ASN A 88 1 13 HELIX 3 AA3 LYS A 98 LEU A 100 5 3 HELIX 4 AA4 SER A 147 PHE A 158 1 12 HELIX 5 AA5 ASN A 169 GLN A 180 1 12 HELIX 6 AA6 THR A 190 MET A 196 1 7 HELIX 7 AA7 TRP A 198 VAL A 202 5 5 HELIX 8 AA8 ASP A 228 GLY A 236 1 9 HELIX 9 AA9 VAL A 237 HIS A 239 5 3 HELIX 10 AB1 ASP A 240 GLU A 258 1 19 HELIX 11 AB2 PRO A 324 LYS A 345 1 22 HELIX 12 AB3 GLY A 346 ASP A 352 1 7 HELIX 13 AB4 SER B 28 TYR B 46 1 19 HELIX 14 AB5 LEU B 76 ASN B 88 1 13 HELIX 15 AB6 LYS B 98 LEU B 100 5 3 HELIX 16 AB7 PRO B 127 VAL B 130 5 4 HELIX 17 AB8 SER B 147 PHE B 158 1 12 HELIX 18 AB9 ASN B 169 GLN B 181 1 13 HELIX 19 AC1 THR B 190 GLY B 197 1 8 HELIX 20 AC2 TRP B 198 VAL B 202 5 5 HELIX 21 AC3 ASP B 228 GLY B 236 1 9 HELIX 22 AC4 VAL B 237 HIS B 239 5 3 HELIX 23 AC5 ASP B 240 LEU B 257 1 18 HELIX 24 AC6 PRO B 324 LYS B 345 1 22 HELIX 25 AC7 GLY B 346 ASP B 352 1 7 SHEET 1 AA1 5 PHE A 51 MET A 56 0 SHEET 2 AA1 5 ILE A 21 ARG A 26 1 N VAL A 23 O ILE A 54 SHEET 3 AA1 5 LEU A 92 SER A 96 1 O LEU A 92 N GLY A 24 SHEET 4 AA1 5 LEU A 220 ARG A 225 -1 O GLY A 221 N HIS A 95 SHEET 5 AA1 5 PHE A 108 ILE A 113 -1 N ALA A 112 O VAL A 222 SHEET 1 AA2 5 GLU A 162 ARG A 164 0 SHEET 2 AA2 5 VAL A 142 GLY A 144 1 N VAL A 143 O GLU A 162 SHEET 3 AA2 5 ALA A 185 ALA A 189 1 O ALA A 185 N GLY A 144 SHEET 4 AA2 5 ASP A 121 PHE A 125 -1 N ALA A 122 O LEU A 188 SHEET 5 AA2 5 GLN A 204 ILE A 205 -1 O GLN A 204 N VAL A 123 SHEET 1 AA3 3 VAL A 265 LYS A 272 0 SHEET 2 AA3 3 GLN A 275 TRP A 283 -1 O THR A 279 N HIS A 268 SHEET 3 AA3 3 SER A 290 THR A 298 -1 O MET A 295 N LEU A 278 SHEET 1 AA4 5 PHE B 51 MET B 56 0 SHEET 2 AA4 5 ILE B 21 ARG B 26 1 N THR B 25 O ILE B 54 SHEET 3 AA4 5 LEU B 92 SER B 96 1 O LEU B 92 N GLY B 24 SHEET 4 AA4 5 LEU B 220 ARG B 225 -1 O GLY B 221 N HIS B 95 SHEET 5 AA4 5 PHE B 108 ILE B 113 -1 N ALA B 112 O VAL B 222 SHEET 1 AA5 5 GLU B 162 ARG B 164 0 SHEET 2 AA5 5 VAL B 142 GLY B 144 1 N VAL B 143 O GLU B 162 SHEET 3 AA5 5 ALA B 185 ALA B 189 1 O ALA B 185 N GLY B 144 SHEET 4 AA5 5 ASP B 121 PHE B 125 -1 N ALA B 122 O LEU B 188 SHEET 5 AA5 5 GLN B 204 ILE B 205 -1 O GLN B 204 N VAL B 123 SHEET 1 AA6 3 VAL B 265 LYS B 272 0 SHEET 2 AA6 3 GLN B 275 TRP B 283 -1 O THR B 279 N HIS B 268 SHEET 3 AA6 3 SER B 290 THR B 298 -1 O MET B 295 N LEU B 278 LINK SG CYS A 261 CHA DPM A 401 1555 1555 1.78 LINK SG CYS B 261 CHA DPM B 401 1555 1555 1.81 SITE 1 AC1 16 SER A 96 LYS A 98 ASP A 99 SER A 146 SITE 2 AC1 16 SER A 147 ARG A 149 ARG A 150 ARG A 173 SITE 3 AC1 16 ALA A 189 ARG A 195 GLN A 217 GLY A 218 SITE 4 AC1 16 CYS A 261 HOH A 504 HOH A 509 HOH A 516 SITE 1 AC2 4 HIS A 300 PRO A 302 ALA A 303 GLN A 304 SITE 1 AC3 2 PRO A 119 ARG A 246 SITE 1 AC4 3 ILE A 299 HIS A 300 PRO A 327 SITE 1 AC5 4 HIS B 300 PRO B 302 ALA B 303 GLN B 304 SITE 1 AC6 3 PRO B 119 HIS B 120 ARG B 246 SITE 1 AC7 2 GLN B 29 ASN B 169 SITE 1 AC8 19 SER B 96 LYS B 98 ASP B 99 THR B 145 SITE 2 AC8 19 SER B 146 SER B 147 ARG B 149 ARG B 150 SITE 3 AC8 19 ARG B 173 LEU B 188 ALA B 189 ARG B 195 SITE 4 AC8 19 GLN B 217 GLY B 218 GLY B 260 SER B 262 SITE 5 AC8 19 VAL B 263 HOH B 503 HOH B 507 CRYST1 70.420 80.950 76.220 90.00 95.70 90.00 P 1 21 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 0.014201 0.000000 0.001417 0.00000 SCALE2 0.000000 0.012353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013185 0.00000