HEADER PHOTOSYNTHESIS 06-JUN-23 8JNN TITLE LINKER PROTEIN LPP1 FROM RED ALGAL PORPHYRIDIUM PURPUREUM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LPP1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYRIDIUM PURPUREUM; SOURCE 3 ORGANISM_TAXID: 35688; SOURCE 4 GENE: FVE85_8359; SOURCE 5 EXPRESSION_SYSTEM: PORPHYRIDIUM PURPUREUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 35688 KEYWDS LPP1, PHOTOSYNTHESIS EXPDTA ELECTRON MICROSCOPY AUTHOR X.YOU,X.ZHANG,J.CHENG,Y.N.XIAO,S.SUN,S.F.SUI REVDAT 2 03-JUL-24 8JNN 1 REMARK REVDAT 1 02-AUG-23 8JNN 0 JRNL AUTH X.YOU,X.ZHANG,J.CHENG,Y.N.XIAO,S.SUN,S.F.SUI JRNL TITL STRUCTURE OF LATERAL HEXAMER OF PBS-PSII-PSI-LHCS JRNL TITL 2 MEGACOMPLEX AT 6.3 ANGSTROMS RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 762000 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8JNN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038339. 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 : CELL REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : LINKER PROTEIN LPP1 FROM REMARK 245 PORPHYRIDIUM PURPUREUM. 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 6000.00 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) : 3500.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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 MET A -159 REMARK 465 GLU A -158 REMARK 465 ALA A -157 REMARK 465 PHE A -156 REMARK 465 VAL A -155 REMARK 465 PRO A -154 REMARK 465 GLY A -153 REMARK 465 VAL A -152 REMARK 465 GLY A -151 REMARK 465 PRO A -150 REMARK 465 LEU A -149 REMARK 465 LEU A -148 REMARK 465 GLY A -147 REMARK 465 ALA A -146 REMARK 465 PRO A -145 REMARK 465 ALA A -144 REMARK 465 ALA A -143 REMARK 465 PRO A -142 REMARK 465 LEU A -141 REMARK 465 ALA A -140 REMARK 465 ALA A -139 REMARK 465 VAL A -138 REMARK 465 ASP A -137 REMARK 465 VAL A -136 REMARK 465 ARG A -135 REMARK 465 CYS A -134 REMARK 465 ARG A -133 REMARK 465 HIS A -132 REMARK 465 ALA A -131 REMARK 465 SER A -130 REMARK 465 VAL A -129 REMARK 465 ALA A -128 REMARK 465 ARG A -127 REMARK 465 ARG A -126 REMARK 465 ALA A -125 REMARK 465 ARG A -124 REMARK 465 VAL A -123 REMARK 465 ALA A -122 REMARK 465 VAL A -121 REMARK 465 ARG A -120 REMARK 465 MET A -119 REMARK 465 ALA A -118 REMARK 465 ASP A -117 REMARK 465 ASP A -116 REMARK 465 GLY A -115 REMARK 465 PHE A -114 REMARK 465 ALA A -113 REMARK 465 ASP A -112 REMARK 465 LEU A -111 REMARK 465 GLN A -110 REMARK 465 PRO A -109 REMARK 465 GLY A -108 REMARK 465 ASP A -107 REMARK 465 PRO A -106 REMARK 465 GLY A -105 REMARK 465 TYR A -104 REMARK 465 LYS A -103 REMARK 465 PRO A -102 REMARK 465 LYS A -101 REMARK 465 ALA A -100 REMARK 465 LYS A -99 REMARK 465 GLU A -98 REMARK 465 MET A -97 REMARK 465 VAL A -96 REMARK 465 LYS A -95 REMARK 465 VAL A -94 REMARK 465 SER A -93 REMARK 465 GLU A -92 REMARK 465 LEU A -91 REMARK 465 GLY A -90 REMARK 465 VAL A -89 REMARK 465 SER A -88 REMARK 465 PRO A -87 REMARK 465 PHE A -86 REMARK 465 SER A -85 REMARK 465 ASP A -84 REMARK 465 ASP A -83 REMARK 465 ALA A -82 REMARK 465 ASN A -81 REMARK 465 SER A -80 REMARK 465 VAL A -79 REMARK 465 THR A -78 REMARK 465 ARG A -77 REMARK 465 LEU A -76 REMARK 465 GLY A -75 REMARK 465 GLU A -74 REMARK 465 GLY A -73 REMARK 465 ARG A -72 REMARK 465 LEU A -71 REMARK 465 ASP A -70 REMARK 465 GLU A -69 REMARK 465 ILE A -68 REMARK 465 ALA A -67 REMARK 465 LYS A -66 REMARK 465 ASP A -65 REMARK 465 ILE A -64 REMARK 465 MET A -63 REMARK 465 GLU A -62 REMARK 465 GLY A -61 REMARK 465 LYS A -60 REMARK 465 LYS A -59 REMARK 465 THR A -58 REMARK 465 GLY A -57 REMARK 465 ALA A -56 REMARK 465 GLU A -55 REMARK 465 ILE A -54 REMARK 465 LYS A -53 REMARK 465 ALA A -52 REMARK 465 ASP A -51 REMARK 465 LEU A -50 REMARK 465 LYS A -49 REMARK 465 LYS A -48 REMARK 465 GLN A -47 REMARK 465 ALA A -46 REMARK 465 PRO A -45 REMARK 465 ALA A -44 REMARK 465 LYS A -43 REMARK 465 PRO A -42 REMARK 465 ALA A -41 REMARK 465 ALA A -40 REMARK 465 PRO A -39 REMARK 465 ALA A -38 REMARK 465 LYS A -37 REMARK 465 LYS A -36 REMARK 465 PRO A -35 REMARK 465 GLU A -34 REMARK 465 LYS A -33 REMARK 465 LYS A -32 REMARK 465 SER A -31 REMARK 465 GLY A -30 REMARK 465 LEU A -29 REMARK 465 ALA A -28 REMARK 465 SER A -27 REMARK 465 ALA A -26 REMARK 465 LYS A -25 REMARK 465 ASP A -24 REMARK 465 ALA A -23 REMARK 465 ALA A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 ALA A -19 REMARK 465 MET A -18 REMARK 465 GLY A -17 REMARK 465 ALA A -16 REMARK 465 VAL A -15 REMARK 465 GLN A -14 REMARK 465 ARG A -13 REMARK 465 ALA A -12 REMARK 465 VAL A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LYS A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 LEU A -4 REMARK 465 ASP A -3 REMARK 465 LEU A -2 REMARK 465 LEU A -1 REMARK 465 ARG A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 47 CA SER A 47 CB -0.135 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 2 -157.96 -145.46 REMARK 500 LEU A 4 127.71 -39.79 REMARK 500 THR A 6 73.54 55.63 REMARK 500 ARG A 15 -53.26 -120.97 REMARK 500 ASP A 17 -60.74 -95.52 REMARK 500 LEU A 108 -3.04 66.27 REMARK 500 VAL A 131 125.80 -38.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 45 14.92 REMARK 500 SER A 47 -16.86 REMARK 500 PHE A 49 -10.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33605 RELATED DB: EMDB DBREF1 8JNN A -159 133 UNP A0A5J4YN73_PORPP DBREF2 8JNN A A0A5J4YN73 1 293 SEQRES 1 A 293 MET GLU ALA PHE VAL PRO GLY VAL GLY PRO LEU LEU GLY SEQRES 2 A 293 ALA PRO ALA ALA PRO LEU ALA ALA VAL ASP VAL ARG CYS SEQRES 3 A 293 ARG HIS ALA SER VAL ALA ARG ARG ALA ARG VAL ALA VAL SEQRES 4 A 293 ARG MET ALA ASP ASP GLY PHE ALA ASP LEU GLN PRO GLY SEQRES 5 A 293 ASP PRO GLY TYR LYS PRO LYS ALA LYS GLU MET VAL LYS SEQRES 6 A 293 VAL SER GLU LEU GLY VAL SER PRO PHE SER ASP ASP ALA SEQRES 7 A 293 ASN SER VAL THR ARG LEU GLY GLU GLY ARG LEU ASP GLU SEQRES 8 A 293 ILE ALA LYS ASP ILE MET GLU GLY LYS LYS THR GLY ALA SEQRES 9 A 293 GLU ILE LYS ALA ASP LEU LYS LYS GLN ALA PRO ALA LYS SEQRES 10 A 293 PRO ALA ALA PRO ALA LYS LYS PRO GLU LYS LYS SER GLY SEQRES 11 A 293 LEU ALA SER ALA LYS ASP ALA ALA GLY SER ALA MET GLY SEQRES 12 A 293 ALA VAL GLN ARG ALA VAL GLY SER GLY LYS ARG GLY LEU SEQRES 13 A 293 ASP LEU LEU ARG GLU ASP PHE LEU GLN THR GLY PRO GLU SEQRES 14 A 293 ARG ALA GLY VAL GLY ARG GLN ASP LYS THR VAL ASP ALA SEQRES 15 A 293 PRO PRO GLN PHE GLY GLU PRO GLY TYR VAL THR PRO ALA SEQRES 16 A 293 TYR GLN ARG VAL LYS VAL SER SER LEU GLY ILE SER VAL SEQRES 17 A 293 PHE GLU ASP ASP ALA ASN ALA VAL THR LYS VAL GLY GLY SEQRES 18 A 293 ILE LYS ALA VAL MET GLU VAL ALA GLU LYS VAL ALA SER SEQRES 19 A 293 GLY GLU LEU LYS THR GLU GLU PHE GLU GLU GLY LEU LYS SEQRES 20 A 293 ALA GLY LEU SER LEU ASP LEU ALA LEU GLU LYS MET GLU SEQRES 21 A 293 GLU GLU ALA ALA ALA GLY ASP LEU LEU PRO ASP TYR LEU SEQRES 22 A 293 LYS PRO LEU PRO GLU ASP THR PRO ARG LYS GLY MET THR SEQRES 23 A 293 TRP LYS ASN TYR VAL GLY ARG HELIX 1 AA1 THR A 6 ALA A 11 5 6 HELIX 2 AA2 LYS A 40 LEU A 44 5 5 HELIX 3 AA3 GLY A 60 SER A 74 1 15 HELIX 4 AA4 LYS A 78 ALA A 88 1 11 HELIX 5 AA5 SER A 91 GLU A 101 1 11 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 TER 1012 ARG A 133 MASTER 322 0 0 5 0 0 0 6 1011 1 0 23 END