HEADER CYTOSOLIC PROTEIN 15-JAN-19 6J6K TITLE APO-STATE STREPTAVIDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTAVIDIN; COMPND 3 CHAIN: A, B, C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVIDINII; SOURCE 3 ORGANISM_TAXID: 1895 KEYWDS STREPTAVIDIN, CYTOSOLIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.FAN,J.WANG,J.L.LEI,H.W.WANG REVDAT 5 27-MAR-24 6J6K 1 REMARK REVDAT 4 05-AUG-20 6J6K 1 REMARK REVDAT 3 06-NOV-19 6J6K 1 CRYST1 SCALE REVDAT 2 19-JUN-19 6J6K 1 JRNL REVDAT 1 29-MAY-19 6J6K 0 JRNL AUTH X.FAN,J.WANG,X.ZHANG,Z.YANG,J.C.ZHANG,L.ZHAO,H.L.PENG,J.LEI, JRNL AUTH 2 H.W.WANG JRNL TITL SINGLE PARTICLE CRYO-EM RECONSTRUCTION OF 52 KDA JRNL TITL 2 STREPTAVIDIN AT 3.2 ANGSTROM RESOLUTION. JRNL REF NAT COMMUN V. 10 2386 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31160591 JRNL DOI 10.1038/S41467-019-10368-W REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH, RELION, RELION, RELION, REMARK 3 RELION, RELION 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 : 23991 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 6J6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010553. 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 : STREPTAVIDIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1450 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : -800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : -800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.01 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 215000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 45 OG REMARK 470 ASP A 128 CG OD1 OD2 REMARK 470 SER B 45 OG REMARK 470 ASP B 128 CG OD1 OD2 REMARK 470 SER C 45 OG REMARK 470 ASP C 128 CG OD1 OD2 REMARK 470 SER D 45 OG REMARK 470 ASP D 128 CG OD1 OD2 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 SER A 45 104.34 65.71 REMARK 500 ALA A 46 -133.06 -22.95 REMARK 500 VAL A 47 -38.92 3.70 REMARK 500 ASP A 67 49.39 -92.85 REMARK 500 ASN A 118 32.35 -95.24 REMARK 500 SER B 45 104.35 65.60 REMARK 500 ALA B 46 -133.12 -22.79 REMARK 500 VAL B 47 -38.80 3.60 REMARK 500 ASP B 67 49.30 -92.72 REMARK 500 ASN B 118 32.25 -95.21 REMARK 500 SER C 45 104.34 65.64 REMARK 500 ALA C 46 -133.09 -22.93 REMARK 500 VAL C 47 -38.82 3.63 REMARK 500 ASP C 67 49.38 -92.73 REMARK 500 ASN C 118 32.32 -95.24 REMARK 500 SER D 45 104.36 65.59 REMARK 500 ALA D 46 -133.11 -22.79 REMARK 500 VAL D 47 -38.86 3.68 REMARK 500 ASP D 67 49.33 -92.76 REMARK 500 ASN D 118 32.34 -95.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 45 ALA A 46 -141.63 REMARK 500 ALA A 46 VAL A 47 -99.24 REMARK 500 SER B 45 ALA B 46 -141.68 REMARK 500 ALA B 46 VAL B 47 -99.18 REMARK 500 SER C 45 ALA C 46 -141.62 REMARK 500 ALA C 46 VAL C 47 -99.21 REMARK 500 SER D 45 ALA D 46 -141.68 REMARK 500 ALA D 46 VAL D 47 -99.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-0689 RELATED DB: EMDB REMARK 900 THE SAME PROTEIN WITH BIOTIN REMARK 900 RELATED ID: EMD-0690 RELATED DB: EMDB REMARK 900 APO-STATE STREPTAVIDIN DBREF 6J6K A 16 134 UNP P22629 SAV_STRAV 40 158 DBREF 6J6K B 16 134 UNP P22629 SAV_STRAV 40 158 DBREF 6J6K C 16 134 UNP P22629 SAV_STRAV 40 158 DBREF 6J6K D 16 134 UNP P22629 SAV_STRAV 40 158 SEQRES 1 A 119 GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SER THR SEQRES 2 A 119 PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU THR GLY SEQRES 3 A 119 THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER ARG TYR SEQRES 4 A 119 VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA THR ASP SEQRES 5 A 119 GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA TRP LYS SEQRES 6 A 119 ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR TRP SER SEQRES 7 A 119 GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE ASN THR SEQRES 8 A 119 GLN TRP LEU LEU THR SER GLY THR THR GLU ALA ASN ALA SEQRES 9 A 119 TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE THR LYS SEQRES 10 A 119 VAL LYS SEQRES 1 B 119 GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SER THR SEQRES 2 B 119 PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU THR GLY SEQRES 3 B 119 THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER ARG TYR SEQRES 4 B 119 VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA THR ASP SEQRES 5 B 119 GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA TRP LYS SEQRES 6 B 119 ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR TRP SER SEQRES 7 B 119 GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE ASN THR SEQRES 8 B 119 GLN TRP LEU LEU THR SER GLY THR THR GLU ALA ASN ALA SEQRES 9 B 119 TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE THR LYS SEQRES 10 B 119 VAL LYS SEQRES 1 C 119 GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SER THR SEQRES 2 C 119 PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU THR GLY SEQRES 3 C 119 THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER ARG TYR SEQRES 4 C 119 VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA THR ASP SEQRES 5 C 119 GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA TRP LYS SEQRES 6 C 119 ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR TRP SER SEQRES 7 C 119 GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE ASN THR SEQRES 8 C 119 GLN TRP LEU LEU THR SER GLY THR THR GLU ALA ASN ALA SEQRES 9 C 119 TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE THR LYS SEQRES 10 C 119 VAL LYS SEQRES 1 D 119 GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SER THR SEQRES 2 D 119 PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU THR GLY SEQRES 3 D 119 THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER ARG TYR SEQRES 4 D 119 VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA THR ASP SEQRES 5 D 119 GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA TRP LYS SEQRES 6 D 119 ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR TRP SER SEQRES 7 D 119 GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE ASN THR SEQRES 8 D 119 GLN TRP LEU LEU THR SER GLY THR THR GLU ALA ASN ALA SEQRES 9 D 119 TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE THR LYS SEQRES 10 D 119 VAL LYS SHEET 1 AA1 8 GLY A 19 TRP A 21 0 SHEET 2 AA1 8 PHE A 29 ALA A 33 -1 O PHE A 29 N TRP A 21 SHEET 3 AA1 8 ALA A 38 TYR A 43 -1 O THR A 40 N THR A 32 SHEET 4 AA1 8 TYR A 54 TYR A 60 -1 O TYR A 54 N TYR A 43 SHEET 5 AA1 8 THR A 71 LYS A 80 -1 O THR A 76 N THR A 57 SHEET 6 AA1 8 ASN A 85 VAL A 97 -1 O THR A 90 N VAL A 77 SHEET 7 AA1 8 ARG A 103 SER A 112 -1 O ARG A 103 N VAL A 97 SHEET 8 AA1 8 GLY A 126 PHE A 130 -1 O PHE A 130 N ILE A 104 SHEET 1 AA2 8 GLY B 19 TRP B 21 0 SHEET 2 AA2 8 PHE B 29 ALA B 33 -1 O PHE B 29 N TRP B 21 SHEET 3 AA2 8 ALA B 38 TYR B 43 -1 O THR B 40 N THR B 32 SHEET 4 AA2 8 TYR B 54 TYR B 60 -1 O TYR B 54 N TYR B 43 SHEET 5 AA2 8 THR B 71 LYS B 80 -1 O THR B 76 N THR B 57 SHEET 6 AA2 8 ASN B 85 VAL B 97 -1 O THR B 90 N VAL B 77 SHEET 7 AA2 8 ARG B 103 SER B 112 -1 O ARG B 103 N VAL B 97 SHEET 8 AA2 8 GLY B 126 PHE B 130 -1 O PHE B 130 N ILE B 104 SHEET 1 AA3 8 GLY C 19 TRP C 21 0 SHEET 2 AA3 8 PHE C 29 ALA C 33 -1 O PHE C 29 N TRP C 21 SHEET 3 AA3 8 ALA C 38 TYR C 43 -1 O THR C 40 N THR C 32 SHEET 4 AA3 8 TYR C 54 TYR C 60 -1 O TYR C 54 N TYR C 43 SHEET 5 AA3 8 THR C 71 LYS C 80 -1 O THR C 76 N THR C 57 SHEET 6 AA3 8 ASN C 85 VAL C 97 -1 O THR C 90 N VAL C 77 SHEET 7 AA3 8 ARG C 103 SER C 112 -1 O ARG C 103 N VAL C 97 SHEET 8 AA3 8 GLY C 126 PHE C 130 -1 O PHE C 130 N ILE C 104 SHEET 1 AA4 8 GLY D 19 TRP D 21 0 SHEET 2 AA4 8 PHE D 29 ALA D 33 -1 O PHE D 29 N TRP D 21 SHEET 3 AA4 8 ALA D 38 TYR D 43 -1 O THR D 40 N THR D 32 SHEET 4 AA4 8 TYR D 54 TYR D 60 -1 O TYR D 54 N TYR D 43 SHEET 5 AA4 8 THR D 71 LYS D 80 -1 O THR D 76 N THR D 57 SHEET 6 AA4 8 ASN D 85 VAL D 97 -1 O THR D 90 N VAL D 77 SHEET 7 AA4 8 ARG D 103 SER D 112 -1 O ARG D 103 N VAL D 97 SHEET 8 AA4 8 GLY D 126 PHE D 130 -1 O PHE D 130 N ILE D 104 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