HEADER PHOTOSYNTHESIS 10-JUN-23 8JP3 TITLE FCP TRIMER IN DIATOM THALASSIOSIRA PSEUDONANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUCOXANTHIN CHLOROPHYLL A/C PROTEIN 8; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THALASSIOSIRA PSEUDONANA CCMP1335; SOURCE 3 ORGANISM_TAXID: 296543 KEYWDS FCP TRIMER, PHOTOSYNTHESIS EXPDTA ELECTRON MICROSCOPY AUTHOR Y.FENG,Z.LI,C.C.ZHOU,C.LIU,J.R.SHEN,W.WANG REVDAT 1 12-JUN-24 8JP3 0 JRNL AUTH Y.FENG,Z.LI,C.C.ZHOU,W.WANG,J.R.SHEN JRNL TITL FCP TRIMER IN DIATOM THALASSIOSIRA PSEUDONANA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 2.730 REMARK 3 NUMBER OF PARTICLES : 103596 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 8JP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038509. 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 : FCP TRIMER 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 : 6.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6000.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 ILE A 205 -70.52 64.53 REMARK 500 ILE B 205 -70.43 64.84 REMARK 500 ILE C 205 -70.49 65.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CLA A 308 REMARK 610 CLA A 309 REMARK 610 CLA A 314 REMARK 610 CLA A 316 REMARK 610 CLA A 318 REMARK 610 LMG A 319 REMARK 610 CLA B 308 REMARK 610 CLA B 309 REMARK 610 CLA B 314 REMARK 610 CLA B 316 REMARK 610 CLA B 317 REMARK 610 LMG B 318 REMARK 610 CLA C 309 REMARK 610 CLA C 310 REMARK 610 CLA C 315 REMARK 610 CLA C 317 REMARK 610 CLA C 319 REMARK 610 LMG C 320 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 CLA A 318 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 46 O REMARK 620 2 CLA A 318 NA 66.0 REMARK 620 3 CLA A 318 NB 75.8 92.1 REMARK 620 4 CLA A 318 NC 114.2 176.7 91.1 REMARK 620 5 CLA A 318 ND 105.1 90.7 177.2 86.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CLA A 309 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE2 REMARK 620 2 CLA A 309 NA 87.4 REMARK 620 3 CLA A 309 NB 88.3 91.9 REMARK 620 4 CLA A 309 NC 93.5 176.6 91.5 REMARK 620 5 CLA A 309 ND 92.4 90.7 177.3 85.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 KC2 A 312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 123 OE1 REMARK 620 2 KC2 A 312 NB 90.9 REMARK 620 3 KC2 A 312 ND 89.0 178.9 REMARK 620 4 KC2 A 312 NA 82.5 90.0 88.9 REMARK 620 5 KC2 A 312 NC 97.6 90.5 90.6 179.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CLA B 317 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO B 46 O REMARK 620 2 CLA B 317 NA 66.0 REMARK 620 3 CLA B 317 NB 77.4 92.1 REMARK 620 4 CLA B 317 NC 114.0 176.7 91.1 REMARK 620 5 CLA B 317 ND 103.5 90.6 177.2 86.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CLA B 309 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 66 OE2 REMARK 620 2 CLA B 309 NA 88.2 REMARK 620 3 CLA B 309 NB 87.2 91.9 REMARK 620 4 CLA B 309 NC 92.7 176.6 91.5 REMARK 620 5 CLA B 309 ND 93.6 90.8 177.2 85.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 KC2 B 312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 123 OE1 REMARK 620 2 KC2 B 312 NB 88.5 REMARK 620 3 KC2 B 312 ND 91.4 178.9 REMARK 620 4 KC2 B 312 NA 84.9 90.0 88.9 REMARK 620 5 KC2 B 312 NC 95.1 90.5 90.6 179.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CLA C 319 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO C 46 O REMARK 620 2 CLA C 319 NA 66.7 REMARK 620 3 CLA C 319 NB 75.5 92.1 REMARK 620 4 CLA C 319 NC 113.6 176.7 91.1 REMARK 620 5 CLA C 319 ND 105.4 90.6 177.3 86.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 KC2 C 313 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN C 123 OE1 REMARK 620 2 KC2 C 313 NB 89.0 REMARK 620 3 KC2 C 313 ND 90.8 178.9 REMARK 620 4 KC2 C 313 NA 83.4 90.0 88.9 REMARK 620 5 KC2 C 313 NC 96.6 90.5 90.6 179.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36466 RELATED DB: EMDB REMARK 900 FCP TRIMER IN DIATOM THALASSIOSIRA PSEUDONANA DBREF 8JP3 A 30 209 UNP B8BS67 B8BS67_THAPS 30 209 DBREF 8JP3 B 30 209 UNP B8BS67 B8BS67_THAPS 30 209 DBREF 8JP3 C 30 209 UNP B8BS67 B8BS67_THAPS 30 209 SEQRES 1 A 180 ALA PHE GLU ASP GLU LEU GLY ALA GLN ALA PRO LEU GLY SEQRES 2 A 180 PHE PHE ASP PRO PHE GLY MET LEU SER GLY ASP CYS THR SEQRES 3 A 180 GLN GLU ARG PHE ASP ARG LEU ARG TYR VAL GLU ILE LYS SEQRES 4 A 180 HIS GLY ARG ILE ALA GLN LEU ALA PHE LEU GLY GLN VAL SEQRES 5 A 180 VAL THR ARG ALA GLY ILE HIS LEU PRO GLY SER ILE ASN SEQRES 6 A 180 TYR ALA GLY ASP SER PHE ASP SER PHE PRO ASN GLY VAL SEQRES 7 A 180 ALA ALA LEU PHE GLY PRO ASN SER ILE PRO THR ALA GLY SEQRES 8 A 180 LEU VAL GLN ILE ILE SER PHE ILE GLY ILE LEU GLU CYS SEQRES 9 A 180 ALA PHE MET ARG ASP VAL PRO GLY THR GLY ASN GLU HIS SEQRES 10 A 180 VAL GLY ASP PHE ARG ASN GLY TYR ILE ASP PHE GLY TRP SEQRES 11 A 180 ASP GLU PHE ASP GLU GLU THR LYS LEU SER LYS ARG ALA SEQRES 12 A 180 ILE GLU LEU ASN ASN GLY ARG ALA ALA MET MET GLY ILE SEQRES 13 A 180 LEU GLY LEU MET VAL HIS GLU GLU ILE ILE PRO LEU GLY SEQRES 14 A 180 TYR ASP ALA ASP LEU PRO ILE ILE GLY HIS LEU SEQRES 1 B 180 ALA PHE GLU ASP GLU LEU GLY ALA GLN ALA PRO LEU GLY SEQRES 2 B 180 PHE PHE ASP PRO PHE GLY MET LEU SER GLY ASP CYS THR SEQRES 3 B 180 GLN GLU ARG PHE ASP ARG LEU ARG TYR VAL GLU ILE LYS SEQRES 4 B 180 HIS GLY ARG ILE ALA GLN LEU ALA PHE LEU GLY GLN VAL SEQRES 5 B 180 VAL THR ARG ALA GLY ILE HIS LEU PRO GLY SER ILE ASN SEQRES 6 B 180 TYR ALA GLY ASP SER PHE ASP SER PHE PRO ASN GLY VAL SEQRES 7 B 180 ALA ALA LEU PHE GLY PRO ASN SER ILE PRO THR ALA GLY SEQRES 8 B 180 LEU VAL GLN ILE ILE SER PHE ILE GLY ILE LEU GLU CYS SEQRES 9 B 180 ALA PHE MET ARG ASP VAL PRO GLY THR GLY ASN GLU HIS SEQRES 10 B 180 VAL GLY ASP PHE ARG ASN GLY TYR ILE ASP PHE GLY TRP SEQRES 11 B 180 ASP GLU PHE ASP GLU GLU THR LYS LEU SER LYS ARG ALA SEQRES 12 B 180 ILE GLU LEU ASN ASN GLY ARG ALA ALA MET MET GLY ILE SEQRES 13 B 180 LEU GLY LEU MET VAL HIS GLU GLU ILE ILE PRO LEU GLY SEQRES 14 B 180 TYR ASP ALA ASP LEU PRO ILE ILE GLY HIS LEU SEQRES 1 C 180 ALA PHE GLU ASP GLU LEU GLY ALA GLN ALA PRO LEU GLY SEQRES 2 C 180 PHE PHE ASP PRO PHE GLY MET LEU SER GLY ASP CYS THR SEQRES 3 C 180 GLN GLU ARG PHE ASP ARG LEU ARG TYR VAL GLU ILE LYS SEQRES 4 C 180 HIS GLY ARG ILE ALA GLN LEU ALA PHE LEU GLY GLN VAL SEQRES 5 C 180 VAL THR ARG ALA GLY ILE HIS LEU PRO GLY SER ILE ASN SEQRES 6 C 180 TYR ALA GLY ASP SER PHE ASP SER PHE PRO ASN GLY VAL SEQRES 7 C 180 ALA ALA LEU PHE GLY PRO ASN SER ILE PRO THR ALA GLY SEQRES 8 C 180 LEU VAL GLN ILE ILE SER PHE ILE GLY ILE LEU GLU CYS SEQRES 9 C 180 ALA PHE MET ARG ASP VAL PRO GLY THR GLY ASN GLU HIS SEQRES 10 C 180 VAL GLY ASP PHE ARG ASN GLY TYR ILE ASP PHE GLY TRP SEQRES 11 C 180 ASP GLU PHE ASP GLU GLU THR LYS LEU SER LYS ARG ALA SEQRES 12 C 180 ILE GLU LEU ASN ASN GLY ARG ALA ALA MET MET GLY ILE SEQRES 13 C 180 LEU GLY LEU MET VAL HIS GLU GLU ILE ILE PRO LEU GLY SEQRES 14 C 180 TYR ASP ALA ASP LEU PRO ILE ILE GLY HIS LEU HET A86 A 301 48 HET A86 A 302 48 HET A86 A 303 48 HET A86 A 304 48 HET A86 A 305 48 HET A86 A 306 48 HET A86 A 307 48 HET CLA A 308 58 HET CLA A 309 53 HET KC2 A 310 45 HET CLA A 311 65 HET KC2 A 312 45 HET CLA A 313 65 HET CLA A 314 59 HET KC1 A 315 45 HET CLA A 316 53 HET CLA A 317 65 HET CLA A 318 61 HET LMG A 319 34 HET A86 B 301 48 HET A86 B 302 48 HET A86 B 303 48 HET A86 B 304 48 HET A86 B 305 48 HET A86 B 306 48 HET A86 B 307 48 HET CLA B 308 58 HET CLA B 309 53 HET KC2 B 310 45 HET CLA B 311 65 HET KC2 B 312 45 HET CLA B 313 65 HET CLA B 314 59 HET KC1 B 315 45 HET CLA B 316 53 HET CLA B 317 61 HET LMG B 318 34 HET CLA C 301 65 HET A86 C 302 48 HET A86 C 303 48 HET A86 C 304 48 HET A86 C 305 48 HET A86 C 306 48 HET A86 C 307 48 HET A86 C 308 48 HET CLA C 309 58 HET CLA C 310 53 HET KC2 C 311 45 HET CLA C 312 65 HET KC2 C 313 45 HET CLA C 314 65 HET CLA C 315 59 HET KC1 C 316 45 HET CLA C 317 53 HET CLA C 318 65 HET CLA C 319 61 HET LMG C 320 34 HETNAM A86 (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-DIHYDROXY-8-OXO-6',7'- HETNAM 2 A86 DIDEHYDRO-5,5',6,6',7,8-HEXAHYDRO-5,6-EPOXY-BETA,BETA- HETNAM 3 A86 CAROTEN-3'- YL ACETATE HETNAM CLA CHLOROPHYLL A HETNAM KC2 CHLOROPHYLL C2 HETNAM KC1 CHLOROPHYLL C1 HETNAM LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE HETSYN A86 FUCOXANTHIN FORMUL 4 A86 21(C42 H58 O6) FORMUL 11 CLA 24(C55 H72 MG N4 O5) FORMUL 13 KC2 6(C35 H28 MG N4 O5) FORMUL 18 KC1 3(C35 H30 MG N4 O5) FORMUL 22 LMG 3(C45 H86 O10) HELIX 1 AA1 THR A 55 ALA A 85 1 31 HELIX 2 AA2 SER A 99 PHE A 103 5 5 HELIX 3 AA3 ASN A 105 LEU A 110 5 6 HELIX 4 AA4 PRO A 117 PHE A 135 1 19 HELIX 5 AA5 GLY A 158 PHE A 162 5 5 HELIX 6 AA6 ASP A 163 ILE A 195 1 33 HELIX 7 AA7 THR B 55 ALA B 85 1 31 HELIX 8 AA8 SER B 99 PHE B 103 5 5 HELIX 9 AA9 ASN B 105 LEU B 110 5 6 HELIX 10 AB1 PRO B 117 PHE B 135 1 19 HELIX 11 AB2 GLY B 158 PHE B 162 5 5 HELIX 12 AB3 ASP B 163 ILE B 195 1 33 HELIX 13 AB4 THR C 55 ALA C 85 1 31 HELIX 14 AB5 SER C 99 PHE C 103 5 5 HELIX 15 AB6 ASN C 105 LEU C 110 5 6 HELIX 16 AB7 PRO C 117 PHE C 135 1 19 HELIX 17 AB8 GLY C 158 PHE C 162 5 5 HELIX 18 AB9 ASP C 163 ILE C 195 1 33 LINK O PRO A 46 MG CLA A 318 1555 1555 2.88 LINK OE2 GLU A 66 MG CLA A 309 1555 1555 2.97 LINK OE1 GLN A 123 MG KC2 A 312 1555 1555 2.87 LINK O PRO B 46 MG CLA B 317 1555 1555 2.85 LINK OE2 GLU B 66 MG CLA B 309 1555 1555 2.97 LINK OE1 GLN B 123 MG KC2 B 312 1555 1555 2.87 LINK O PRO C 46 MG CLA C 319 1555 1555 2.88 LINK OE1 GLN C 123 MG KC2 C 313 1555 1555 2.89 CISPEP 1 ALA A 39 PRO A 40 0 -0.62 CISPEP 2 ALA B 39 PRO B 40 0 -1.31 CISPEP 3 ALA C 39 PRO C 40 0 -1.21 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