HEADER TRANSFERASE 28-AUG-17 5OV4 TITLE BACILLUS MEGATERIUM PORPHOBILINOGEN DEAMINASE D82A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PBG,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: BACILLUS MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 GENE: HEMC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEAMINASE, MUTATION, DOMAIN MOVEMENTS, COFACTOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GUO,P.ERSKINE,A.R.COKER,S.P.WOOD,J.B.COOPER REVDAT 4 17-JAN-24 5OV4 1 REMARK REVDAT 3 22-NOV-17 5OV4 1 JRNL REVDAT 2 08-NOV-17 5OV4 1 JRNL REVDAT 1 11-OCT-17 5OV4 0 JRNL AUTH J.GUO,P.ERSKINE,A.R.COKER,S.P.WOOD,J.B.COOPER JRNL TITL STRUCTURAL STUDIES OF DOMAIN MOVEMENT IN ACTIVE-SITE MUTANTS JRNL TITL 2 OF PORPHOBILINOGEN DEAMINASE FROM BACILLUS MEGATERIUM. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 612 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 29095155 JRNL DOI 10.1107/S2053230X17015436 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.5654 - 3.8807 0.99 2691 136 0.1914 0.2265 REMARK 3 2 3.8807 - 3.0812 1.00 2576 119 0.2145 0.2281 REMARK 3 3 3.0812 - 2.6921 0.99 2525 139 0.2492 0.2863 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.80 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 2280 REMARK 3 ANGLE : 0.479 3067 REMARK 3 CHIRALITY : 0.042 351 REMARK 3 PLANARITY : 0.002 397 REMARK 3 DIHEDRAL : 14.254 1420 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5-4.0 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) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 29.564 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 4MLV REMARK 200 REMARK 200 REMARK: CLUSTERS FORMED BY THIN PLATES WITH A DARK YELLOW COLOUR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE PH 3.7, 25 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 24.54600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.69550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.69550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.54600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.24350 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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: 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 PRO A 97 -174.35 -67.90 REMARK 500 ASN A 149 157.51 -47.52 REMARK 500 PRO A 244 73.68 -69.57 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 447 DISTANCE = 7.56 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MLV RELATED DB: PDB REMARK 900 NATIVE PROTEIN DBREF 5OV4 A 1 310 UNP Q8GCA8 Q8GCA8_BACME 1 310 SEQADV 5OV4 HIS A 0 UNP Q8GCA8 EXPRESSION TAG SEQADV 5OV4 ALA A 82 UNP Q8GCA8 ASP 82 ENGINEERED MUTATION SEQRES 1 A 311 HIS MET ARG LYS ILE ILE VAL GLY SER ARG ARG SER LYS SEQRES 2 A 311 LEU ALA LEU THR GLN THR LYS TRP VAL ILE GLU GLN LEU SEQRES 3 A 311 LYS LYS GLN GLY LEU PRO PHE GLU PHE GLU ILE LYS GLU SEQRES 4 A 311 MET VAL THR LYS GLY ASP GLN ILE LEU ASN VAL THR LEU SEQRES 5 A 311 SER LYS VAL GLY GLY LYS GLY LEU PHE VAL LYS GLU ILE SEQRES 6 A 311 GLU GLN ALA MET LEU ASP LYS GLU ILE ASP MET ALA VAL SEQRES 7 A 311 HIS SER MET LYS ALA MET PRO ALA VAL LEU PRO GLU GLY SEQRES 8 A 311 LEU THR ILE GLY CYS ILE PRO LEU ARG GLU ASP HIS ARG SEQRES 9 A 311 ASP ALA LEU ILE SER LYS ASN GLY GLU ARG PHE GLU GLU SEQRES 10 A 311 LEU PRO SER GLY ALA VAL ILE GLY THR SER SER LEU ARG SEQRES 11 A 311 ARG GLY ALA GLN LEU LEU SER MET ARG SER ASP ILE GLU SEQRES 12 A 311 ILE LYS TRP ILE ARG GLY ASN ILE ASP THR ARG LEU GLU SEQRES 13 A 311 LYS LEU LYS ASN GLU ASP TYR ASP ALA ILE ILE LEU ALA SEQRES 14 A 311 ALA ALA GLY LEU SER ARG MET GLY TRP SER LYS ASP THR SEQRES 15 A 311 VAL THR GLN TYR LEU GLU PRO GLU ILE SER VAL PRO ALA SEQRES 16 A 311 VAL GLY GLN GLY ALA LEU ALA ILE GLU CYS ARG GLU ASN SEQRES 17 A 311 ASP HIS GLU LEU LEU SER LEU LEU GLN ALA LEU ASN HIS SEQRES 18 A 311 ASP GLU THR ALA ARG ALA VAL ARG ALA GLU ARG VAL PHE SEQRES 19 A 311 LEU LYS GLU MET GLU GLY GLY CYS GLN VAL PRO ILE ALA SEQRES 20 A 311 GLY TYR GLY ARG ILE LEU ASP GLY GLY ASN ILE GLU LEU SEQRES 21 A 311 THR SER LEU VAL ALA SER PRO ASP GLY LYS THR ILE TYR SEQRES 22 A 311 LYS GLU HIS ILE THR GLY LYS ASP PRO ILE ALA ILE GLY SEQRES 23 A 311 SER GLU ALA ALA GLU ARG LEU THR SER GLN GLY ALA LYS SEQRES 24 A 311 LEU LEU ILE ASP ARG VAL LYS GLU GLU LEU ASP LYS FORMUL 2 HOH *47(H2 O) HELIX 1 AA1 SER A 11 LYS A 27 1 17 HELIX 2 AA2 LYS A 62 ASP A 70 1 9 HELIX 3 AA3 LYS A 81 MET A 83 5 3 HELIX 4 AA4 SER A 127 ARG A 138 1 12 HELIX 5 AA5 ASN A 149 GLU A 160 1 12 HELIX 6 AA6 ALA A 169 MET A 175 1 7 HELIX 7 AA7 SER A 178 VAL A 182 5 5 HELIX 8 AA8 ASP A 208 ALA A 217 1 10 HELIX 9 AA9 HIS A 220 MET A 237 1 18 HELIX 10 AB1 ASP A 280 GLN A 295 1 16 HELIX 11 AB2 GLY A 296 LEU A 308 1 13 SHEET 1 AA1 5 GLU A 33 GLU A 38 0 SHEET 2 AA1 5 LYS A 3 SER A 8 1 N ILE A 4 O GLU A 33 SHEET 3 AA1 5 MET A 75 SER A 79 1 O MET A 75 N GLY A 7 SHEET 4 AA1 5 LEU A 200 ARG A 205 -1 O ALA A 201 N HIS A 78 SHEET 5 AA1 5 LEU A 91 CYS A 95 -1 N THR A 92 O CYS A 204 SHEET 1 AA2 5 GLU A 142 LYS A 144 0 SHEET 2 AA2 5 VAL A 122 GLY A 124 1 N ILE A 123 O GLU A 142 SHEET 3 AA2 5 ALA A 164 ALA A 168 1 O ALA A 164 N GLY A 124 SHEET 4 AA2 5 ASP A 104 SER A 108 -1 N ALA A 105 O LEU A 167 SHEET 5 AA2 5 GLN A 184 LEU A 186 -1 O GLN A 184 N LEU A 106 SHEET 1 AA3 3 ILE A 245 ILE A 251 0 SHEET 2 AA3 3 ILE A 257 ALA A 264 -1 O LEU A 262 N ALA A 246 SHEET 3 AA3 3 ILE A 271 GLY A 278 -1 O TYR A 272 N VAL A 263 CRYST1 49.092 62.487 91.391 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 0.020370 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016003 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010942 0.00000