HEADER OXIDOREDUCTASE 17-NOV-22 8F6T TITLE CRYO-EM STRUCTURE OF ALKANE 1-MONOOXYGENASE ALKB-ALKG COMPLEX FROM TITLE 2 FONTIMONAS THERMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKANE 1-MONOOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.15.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FONTIMONAS THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 1076937; SOURCE 4 GENE: SAMN04488120_10311; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSFER COMPLEX, IRON-SULFUR CLUSTER, HISTIDINE-DIIRON KEYWDS 2 CENTER, HYDROPHOBIC ALKANE BINDING POCKET, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR J.CHAI,G.GUO,S.MCSWEENEY,J.SHANKLIN,Q.LIU REVDAT 3 26-APR-23 8F6T 1 JRNL REVDAT 2 12-APR-23 8F6T 1 JRNL REVDAT 1 05-APR-23 8F6T 0 JRNL AUTH J.CHAI,G.GUO,S.M.MCSWEENEY,J.SHANKLIN,Q.LIU JRNL TITL STRUCTURAL BASIS FOR ENZYMATIC TERMINAL C-H BOND JRNL TITL 2 FUNCTIONALIZATION OF ALKANES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 521 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 36997762 JRNL DOI 10.1038/S41594-023-00958-0 REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.760 REMARK 3 NUMBER OF PARTICLES : 46953 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8F6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000270099. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : ELECTRON TRANSFER COMPLEX OF REMARK 245 ALKB AND ALKG REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 LEU A 6 REMARK 465 ASP A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 THR A 10 REMARK 465 LEU A 11 REMARK 465 ALA A 12 REMARK 465 ARG A 388 REMARK 465 PRO A 389 REMARK 465 ASP A 390 REMARK 465 ALA A 391 REMARK 465 ARG A 392 REMARK 465 ARG A 393 REMARK 465 ALA A 394 REMARK 465 ASP A 395 REMARK 465 THR A 396 REMARK 465 GLN A 397 REMARK 465 PRO A 398 REMARK 465 THR A 399 REMARK 465 ASP A 400 REMARK 465 ALA A 401 REMARK 465 THR A 402 REMARK 465 ALA A 403 REMARK 465 THR A 404 REMARK 465 PRO A 405 REMARK 465 ALA A 406 REMARK 465 ASP A 407 REMARK 465 ALA A 408 REMARK 465 ALA A 409 REMARK 465 ALA A 410 REMARK 465 SER A 411 REMARK 465 PRO A 412 REMARK 465 GLY A 413 REMARK 465 GLY A 414 REMARK 465 ALA A 468 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 59 41.43 -82.92 REMARK 500 PRO A 95 40.72 -82.85 REMARK 500 PRO A 178 1.88 -66.36 REMARK 500 PRO A 181 41.84 -84.89 REMARK 500 HIS A 311 45.69 -86.80 REMARK 500 SER A 312 -54.44 -121.74 REMARK 500 PRO A 318 43.61 -77.47 REMARK 500 PRO A 344 41.23 -79.02 REMARK 500 LEU A 367 50.12 -91.35 REMARK 500 PRO A 452 40.58 -86.52 REMARK 500 REMARK 500 REMARK: NULL 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 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 137 NE2 REMARK 620 2 HIS A 141 NE2 90.4 REMARK 620 3 HIS A 167 NE2 85.5 97.5 REMARK 620 4 HIS A 172 NE2 164.5 94.9 79.3 REMARK 620 5 HIS A 314 NE2 86.6 109.5 152.0 105.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 171 NE2 REMARK 620 2 GLU A 271 OE1 130.9 REMARK 620 3 HIS A 272 NE2 103.0 85.8 REMARK 620 4 HIS A 311 NE2 151.5 68.5 98.8 REMARK 620 5 HIS A 315 NE2 71.0 157.3 95.3 89.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 99.0 REMARK 620 3 CYS A 451 SG 124.1 87.1 REMARK 620 4 CYS A 454 SG 121.5 107.0 108.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28890 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALKANE 1-MONOOXYGENASE ALKB-ALKG COMPLEX FROM REMARK 900 FONTIMONAS THERMOPHILA DBREF1 8F6T A 1 468 UNP A0A1I2I8Z9_9GAMM DBREF2 8F6T A A0A1I2I8Z9 1 468 SEQADV 8F6T SER A -2 UNP A0A1I2I8Z EXPRESSION TAG SEQADV 8F6T ASN A -1 UNP A0A1I2I8Z EXPRESSION TAG SEQADV 8F6T ALA A 0 UNP A0A1I2I8Z EXPRESSION TAG SEQRES 1 A 471 SER ASN ALA MET SER THR PRO THR LEU ASP ALA GLY THR SEQRES 2 A 471 LEU ALA TRP ASN ASP GLY LYS ARG TYR LEU TRP LEU LEU SEQRES 3 A 471 SER PRO PHE ILE PRO VAL LEU GLY LEU ILE GLY LEU GLY SEQRES 4 A 471 LEU PHE LEU TYR THR ASP ILE GLY LEU PHE THR TRP SER SEQRES 5 A 471 GLY PRO LEU LEU ILE TYR GLY LEU ILE PRO LEU LEU ASP SEQRES 6 A 471 TRP LEU VAL GLY GLU ASP ARG ASN ASN PRO PRO GLU ALA SEQRES 7 A 471 ALA VAL ALA GLN LEU GLU ASN ASP ARG TYR TYR ARG ALA SEQRES 8 A 471 ILE VAL TYR ALA TYR LEU PRO THR GLN TYR ALA VAL THR SEQRES 9 A 471 VAL LEU GLY THR TRP VAL ALA VAL THR ALA ASP LEU ALA SEQRES 10 A 471 ILE TRP GLU TYR ILE GLY LEU VAL LEU SER VAL GLY ALA SEQRES 11 A 471 VAL ASN GLY ILE GLY ILE ASN THR ALA HIS GLU LEU GLY SEQRES 12 A 471 HIS LYS ARG GLU ASN LEU ASP ARG TRP LEU ALA LYS LEU SEQRES 13 A 471 THR LEU ALA PRO VAL ALA TYR GLY HIS PHE PHE VAL GLU SEQRES 14 A 471 HIS ASN ARG GLY HIS HIS LYS ASN VAL ALA THR PRO GLU SEQRES 15 A 471 ASP PRO ALA SER SER LYS MET GLY GLU SER PHE TRP ALA SEQRES 16 A 471 PHE LEU PRO ARG THR VAL ILE GLY SER LEU ARG SER ALA SEQRES 17 A 471 TRP ALA ILE GLU LYS ALA ARG LEU GLN ARG ASN LYS GLN SEQRES 18 A 471 SER VAL TRP SER LEU ASP ASN GLU ASN LEU GLN ALA TRP SEQRES 19 A 471 ALA MET THR ILE VAL LEU PHE GLY ALA LEU THR ALA CYS SEQRES 20 A 471 LEU GLY TRP PRO ALA LEU LEU PHE LEU VAL LEU GLN ALA SEQRES 21 A 471 ALA TYR GLY ALA SER LEU LEU GLU VAL ILE ASN TYR ILE SEQRES 22 A 471 GLU HIS TYR GLY LEU LEU ARG GLN LYS LEU PRO ASP GLY SEQRES 23 A 471 ARG TYR GLU ARG CYS GLN PRO ARG HIS SER TRP ASN SER SEQRES 24 A 471 ASN HIS ILE VAL THR ASN LEU PHE LEU TYR GLN LEU GLN SEQRES 25 A 471 ARG HIS SER ASP HIS HIS ALA ASN PRO THR ARG ARG PHE SEQRES 26 A 471 GLN ALA LEU ARG HIS PHE ASP ASP SER PRO GLN LEU PRO SEQRES 27 A 471 SER GLY TYR ALA SER MET LEU ILE PRO ALA TYR VAL PRO SEQRES 28 A 471 TRP LEU TRP PHE ARG LEU MET ASP PRO LEU VAL ALA ARG SEQRES 29 A 471 HIS TYR GLY GLY ASP LEU THR LYS ALA ASN LEU TYR PRO SEQRES 30 A 471 PRO LYS ARG ALA ALA LEU LEU ALA ARG TRP HIS ARG PRO SEQRES 31 A 471 ARG PRO ASP ALA ARG ARG ALA ASP THR GLN PRO THR ASP SEQRES 32 A 471 ALA THR ALA THR PRO ALA ASP ALA ALA ALA SER PRO GLY SEQRES 33 A 471 GLY ARG TYR GLN CYS THR ASP CYS GLY TYR ILE TYR ASP SEQRES 34 A 471 GLU ALA ILE GLY CYS PRO ARG GLU GLY PHE PRO PRO GLY SEQRES 35 A 471 THR PRO TRP SER GLN ILE PRO ASP ASP TRP SER CYS PRO SEQRES 36 A 471 ASP CYS ALA VAL ARG ASP LYS VAL ASP PHE ARG LYS LEU SEQRES 37 A 471 PRO ALA ALA HET FE A 501 1 HET FE A 502 1 HET FE A 503 1 HET D12 A 504 12 HETNAM FE FE (III) ION HETNAM D12 DODECANE FORMUL 2 FE 3(FE 3+) FORMUL 5 D12 C12 H26 HELIX 1 AA1 ARG A 18 PRO A 25 5 8 HELIX 2 AA2 PHE A 26 ASP A 42 1 17 HELIX 3 AA3 ILE A 43 TRP A 48 5 6 HELIX 4 AA4 GLY A 50 GLY A 56 1 7 HELIX 5 AA5 LEU A 57 VAL A 65 1 9 HELIX 6 AA6 PRO A 73 GLU A 81 1 9 HELIX 7 AA7 ARG A 84 ALA A 92 1 9 HELIX 8 AA8 TYR A 93 ALA A 111 1 19 HELIX 9 AA9 ALA A 114 HIS A 141 1 28 HELIX 10 AB1 GLU A 144 LEU A 155 1 12 HELIX 11 AB2 HIS A 162 GLY A 170 1 9 HELIX 12 AB3 SER A 189 ALA A 192 5 4 HELIX 13 AB4 PHE A 193 ASN A 216 1 24 HELIX 14 AB5 ASN A 225 LEU A 245 1 21 HELIX 15 AB6 GLY A 246 HIS A 272 1 27 HELIX 16 AB7 GLN A 289 SER A 293 5 5 HELIX 17 AB8 HIS A 298 LEU A 305 1 8 HELIX 18 AB9 SER A 312 ASN A 317 1 6 HELIX 19 AC1 ARG A 321 LEU A 325 5 5 HELIX 20 AC2 LEU A 342 VAL A 347 1 6 HELIX 21 AC3 VAL A 347 TYR A 363 1 17 HELIX 22 AC4 TYR A 373 PRO A 375 5 3 HELIX 23 AC5 LYS A 376 HIS A 385 1 10 HELIX 24 AC6 PRO A 441 ILE A 445 5 5 HELIX 25 AC7 ASP A 458 PHE A 462 5 5 SHEET 1 AA1 3 ILE A 424 TYR A 425 0 SHEET 2 AA1 3 TYR A 416 GLN A 417 -1 N TYR A 416 O TYR A 425 SHEET 3 AA1 3 ARG A 463 LYS A 464 -1 O ARG A 463 N GLN A 417 LINK NE2 HIS A 137 FE FE A 502 1555 1555 2.27 LINK NE2 HIS A 141 FE FE A 502 1555 1555 2.20 LINK NE2 HIS A 167 FE FE A 502 1555 1555 2.12 LINK NE2 HIS A 171 FE FE A 501 1555 1555 2.47 LINK NE2 HIS A 172 FE FE A 502 1555 1555 2.23 LINK OE1 GLU A 271 FE FE A 501 1555 1555 2.25 LINK NE2 HIS A 272 FE FE A 501 1555 1555 2.16 LINK NE2 HIS A 311 FE FE A 501 1555 1555 2.23 LINK NE2 HIS A 314 FE FE A 502 1555 1555 2.17 LINK NE2 HIS A 315 FE FE A 501 1555 1555 2.42 LINK SG CYS A 418 FE FE A 503 1555 1555 2.30 LINK SG CYS A 421 FE FE A 503 1555 1555 2.29 LINK SG CYS A 451 FE FE A 503 1555 1555 2.30 LINK SG CYS A 454 FE FE A 503 1555 1555 2.29 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000