HEADER OXIDOREDUCTASE 22-AUG-22 8E5J TITLE THE CRYSTAL STRUCTURE OF 4-N-BUTYLBENZOIC ACID BOUND CYP199A4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS HAA2; SOURCE 3 ORGANISM_TAXID: 316058; SOURCE 4 STRAIN: HAA2; SOURCE 5 GENE: RPB_3613; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P450, HEME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.Z.DOHERTY,S.G.BELL,J.B.BRUNING REVDAT 3 20-MAR-24 8E5J 1 JRNL REVDAT 2 13-MAR-24 8E5J 1 COMPND JRNL REMARK HET REVDAT 2 2 1 HETNAM HETSYN FORMUL LINK REVDAT 2 3 1 ATOM REVDAT 1 30-AUG-23 8E5J 0 JRNL AUTH T.COLEMAN,D.Z.DOHERTY,T.ZHANG,M.N.PODGORSKI,R.QIAO, JRNL AUTH 2 J.H.Z.LEE,J.B.BRUNING,J.J.DE VOSS,W.ZHOU,S.G.BELL JRNL TITL EXPLORING THE FACTORS WHICH RESULT IN CYTOCHROME P450 JRNL TITL 2 CATALYZED DESATURATION VERSUS HYDROXYLATION. JRNL REF CHEM ASIAN J V. 17 00986 2022 JRNL REFN ESSN 1861-471X JRNL PMID 36268769 JRNL DOI 10.1002/ASIA.202200986 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 867 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 43.2090 - 4.1788 1.00 2639 154 0.1480 0.1787 REMARK 3 2 4.1788 - 3.3172 1.00 2593 145 0.1373 0.1905 REMARK 3 3 3.3172 - 2.8980 1.00 2561 151 0.1676 0.2280 REMARK 3 4 2.8980 - 2.6331 1.00 2539 151 0.1950 0.2621 REMARK 3 5 2.6331 - 2.4444 1.00 2564 130 0.2036 0.3146 REMARK 3 6 2.4444 - 2.3003 1.00 2581 136 0.2124 0.2839 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.72 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 : 0.004 3168 REMARK 3 ANGLE : 0.687 4327 REMARK 3 CHIRALITY : 0.043 470 REMARK 3 PLANARITY : 0.005 574 REMARK 3 DIHEDRAL : 10.048 2607 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 8E5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16355 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.25400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.00100 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: PHASER REMARK 200 STARTING MODEL: 5UVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 15-30% W/V REMARK 280 PEG3350, 0.1 M BIS-TRIS, PH 5-5.75, VAPOR DIFFUSION, TEMPERATURE REMARK 280 287.15K 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 25.77000 REMARK 290 SMTRY3 2 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 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 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 99 43.84 -108.42 REMARK 500 ILE A 148 -70.20 -80.58 REMARK 500 LEU A 151 -64.03 -135.92 REMARK 500 VAL A 159 -42.18 -131.49 REMARK 500 PHE A 267 79.39 -114.90 REMARK 500 SER A 293 85.39 48.79 REMARK 500 CYS A 358 109.34 -41.48 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 791 DISTANCE = 7.36 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MH0 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 358 SG REMARK 620 2 MH0 A 501 NB 89.9 REMARK 620 3 MH0 A 501 NC 84.2 90.1 REMARK 620 4 MH0 A 501 NA 104.7 88.6 171.0 REMARK 620 5 MH0 A 501 ND 96.7 173.4 90.9 89.5 REMARK 620 N 1 2 3 4 DBREF 8E5J A 17 409 UNP Q2IU02 Q2IU02_RHOP2 18 410 SEQRES 1 A 393 THR ILE PRO HIS LEU ALA ILE ASP PRO PHE SER LEU ASP SEQRES 2 A 393 PHE PHE ASP ASP PRO TYR PRO ASP GLN GLN THR LEU ARG SEQRES 3 A 393 ASP ALA GLY PRO VAL VAL TYR LEU ASP LYS TRP ASN VAL SEQRES 4 A 393 TYR GLY VAL ALA ARG TYR ALA GLU VAL HIS ALA VAL LEU SEQRES 5 A 393 ASN ASP PRO THR THR PHE CYS SER SER ARG GLY VAL GLY SEQRES 6 A 393 LEU SER ASP PHE LYS LYS GLU LYS PRO TRP ARG PRO PRO SEQRES 7 A 393 SER LEU ILE LEU GLU ALA ASP PRO PRO ALA HIS THR ARG SEQRES 8 A 393 PRO ARG ALA VAL LEU SER LYS VAL LEU SER PRO ALA THR SEQRES 9 A 393 MET LYS THR ILE ARG ASP GLY PHE ALA ALA ALA ALA ASP SEQRES 10 A 393 ALA LYS VAL ASP GLU LEU LEU GLN ARG GLY CYS ILE ASP SEQRES 11 A 393 ALA ILE ALA ASP LEU ALA GLU ALA TYR PRO LEU SER VAL SEQRES 12 A 393 PHE PRO ASP ALA MET GLY LEU LYS GLN GLU GLY ARG GLU SEQRES 13 A 393 HIS LEU LEU PRO TYR ALA GLY LEU VAL PHE ASN ALA PHE SEQRES 14 A 393 GLY PRO PRO ASN GLU LEU ARG GLN THR ALA ILE GLU ARG SEQRES 15 A 393 SER ALA PRO HIS GLN ALA TYR VAL ASN GLU GLN CYS GLN SEQRES 16 A 393 ARG PRO ASN LEU ALA PRO GLY GLY PHE GLY ALA CYS ILE SEQRES 17 A 393 HIS ALA PHE THR ASP THR GLY GLU ILE THR PRO ASP GLU SEQRES 18 A 393 ALA PRO LEU LEU VAL ARG SER LEU LEU SER ALA GLY LEU SEQRES 19 A 393 ASP THR THR VAL ASN GLY ILE GLY ALA ALA VAL TYR CYS SEQRES 20 A 393 LEU ALA ARG PHE PRO GLY GLU LEU GLN ARG LEU ARG SER SEQRES 21 A 393 ASP PRO THR LEU ALA ARG ASN ALA PHE GLU GLU ALA VAL SEQRES 22 A 393 ARG PHE GLU SER PRO VAL GLN THR PHE PHE ARG THR THR SEQRES 23 A 393 THR ARG GLU VAL GLU LEU GLY GLY ALA VAL ILE GLY GLU SEQRES 24 A 393 GLY GLU LYS VAL LEU MET PHE LEU GLY SER ALA ASN ARG SEQRES 25 A 393 ASP PRO ARG ARG TRP SER ASP PRO ASP LEU TYR ASP ILE SEQRES 26 A 393 THR ARG LYS THR SER GLY HIS VAL GLY PHE GLY SER GLY SEQRES 27 A 393 VAL HIS MET CYS VAL GLY GLN LEU VAL ALA ARG LEU GLU SEQRES 28 A 393 GLY GLU VAL MET LEU SER ALA LEU ALA ARG LYS VAL ALA SEQRES 29 A 393 ALA ILE ASP ILE ASP GLY PRO VAL LYS ARG ARG PHE ASN SEQRES 30 A 393 ASN THR LEU ARG GLY LEU GLU SER LEU PRO VAL LYS LEU SEQRES 31 A 393 THR PRO ALA HET MH0 A 501 43 HET HX1 A 502 13 HET CL A 503 1 HETNAM MH0 MESOHEME HETNAM HX1 4-BUTYLBENZOIC ACID HETNAM CL CHLORIDE ION FORMUL 2 MH0 C34 H36 FE N4 O4 FORMUL 3 HX1 C11 H14 O2 FORMUL 4 CL CL 1- FORMUL 5 HOH *191(H2 O) HELIX 1 AA1 SER A 27 ASP A 33 1 7 HELIX 2 AA2 PRO A 34 GLY A 45 1 12 HELIX 3 AA3 ARG A 60 ASN A 69 1 10 HELIX 4 AA4 HIS A 105 LEU A 116 1 12 HELIX 5 AA5 SER A 117 GLY A 143 1 27 HELIX 6 AA6 GLU A 153 SER A 158 1 6 HELIX 7 AA7 VAL A 159 GLY A 165 1 7 HELIX 8 AA8 GLY A 170 GLU A 172 5 3 HELIX 9 AA9 HIS A 173 PHE A 185 1 13 HELIX 10 AB1 ASN A 189 GLU A 197 1 9 HELIX 11 AB2 SER A 199 CYS A 210 1 12 HELIX 12 AB3 GLN A 211 LEU A 215 5 5 HELIX 13 AB4 GLY A 219 PHE A 227 1 9 HELIX 14 AB5 GLU A 237 GLY A 249 1 13 HELIX 15 AB6 LEU A 250 PHE A 267 1 18 HELIX 16 AB7 PHE A 267 ASP A 277 1 11 HELIX 17 AB8 LEU A 280 SER A 293 1 14 HELIX 18 AB9 LEU A 323 ASN A 327 1 5 HELIX 19 AC1 GLY A 360 LYS A 378 1 19 SHEET 1 AA1 6 HIS A 20 LEU A 21 0 SHEET 2 AA1 6 VAL A 48 LEU A 50 1 O TYR A 49 N LEU A 21 SHEET 3 AA1 6 TYR A 56 VAL A 58 -1 O GLY A 57 N VAL A 48 SHEET 4 AA1 6 LYS A 318 PHE A 322 1 O LEU A 320 N TYR A 56 SHEET 5 AA1 6 THR A 297 THR A 302 -1 N ARG A 300 O VAL A 319 SHEET 6 AA1 6 PHE A 74 CYS A 75 -1 N CYS A 75 O THR A 301 SHEET 1 AA2 3 CYS A 144 ASP A 146 0 SHEET 2 AA2 3 PRO A 403 PRO A 408 -1 O VAL A 404 N ILE A 145 SHEET 3 AA2 3 VAL A 379 ILE A 384 -1 N ALA A 380 O THR A 407 SHEET 1 AA3 2 VAL A 306 LEU A 308 0 SHEET 2 AA3 2 ALA A 311 ILE A 313 -1 O ALA A 311 N LEU A 308 SHEET 1 AA4 2 LYS A 389 PHE A 392 0 SHEET 2 AA4 2 ARG A 397 SER A 401 -1 O GLU A 400 N LYS A 389 LINK SG CYS A 358 FE MH0 A 501 1555 1555 2.30 CISPEP 1 PRO A 102 PRO A 103 0 3.98 CRYST1 45.010 51.540 79.310 90.00 91.87 90.00 P 1 21 1 2 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 0.022217 0.000000 0.000725 0.00000 SCALE2 0.000000 0.019402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012615 0.00000