HEADER CYTOSOLIC PROTEIN 21-MAR-21 7EFD TITLE 1.77 A CRYO-EM STRUCTURE OF STREPTAVIDIN USING FIRST 40 FRAMES TITLE 2 (CORRESPONDING TO ABOUT 40 E/A^2 TOTAL DOSE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTAVIDIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVIDINII; SOURCE 3 ORGANISM_TAXID: 1895 KEYWDS STREPTAVIDIN, CYTOSOLIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.HIRAIZUMI,K.YAMASHITA,T.NISHIZAWA,A.KOTECHA,O.NUREKI REVDAT 1 28-APR-21 7EFD 0 JRNL AUTH M.HIRAIZUMI JRNL TITL 1.77 A CRYO-EM STRUCTURE OF STREPTAVIDIN USING FIRST 40 JRNL TITL 2 FRAMES (CORRESPONDING TO ABOUT 40E/A^2 TOTAL DOSE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, MOLREP, RELION, RELION, REMARK 3 RELION, REFMAC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5N7X REMARK 3 REFINEMENT SPACE : RECIPROCAL 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) : 1.770 REMARK 3 NUMBER OF PARTICLES : 153976 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 7EFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021330. 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) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4053 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 7000.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 DIHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = D2). 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 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 111.05100 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 111.05100 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 111.05100 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 111.05100 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 111.05100 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 111.05100 REMARK 350 BIOMT3 4 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 -23 REMARK 465 ARG A -22 REMARK 465 LYS A -21 REMARK 465 ILE A -20 REMARK 465 VAL A -19 REMARK 465 VAL A -18 REMARK 465 ALA A -17 REMARK 465 ALA A -16 REMARK 465 ILE A -15 REMARK 465 ALA A -14 REMARK 465 VAL A -13 REMARK 465 SER A -12 REMARK 465 LEU A -11 REMARK 465 THR A -10 REMARK 465 THR A -9 REMARK 465 VAL A -8 REMARK 465 SER A -7 REMARK 465 ILE A -6 REMARK 465 THR A -5 REMARK 465 ALA A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 SER A -1 REMARK 465 ALA A 0 REMARK 465 ASP A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASP A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 GLN A 9 REMARK 465 VAL A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 GLU A 14 REMARK 465 PRO A 135 REMARK 465 SER A 136 REMARK 465 ALA A 137 REMARK 465 ALA A 138 REMARK 465 SER A 139 REMARK 465 ILE A 140 REMARK 465 ASP A 141 REMARK 465 ALA A 142 REMARK 465 ALA A 143 REMARK 465 LYS A 144 REMARK 465 LYS A 145 REMARK 465 ALA A 146 REMARK 465 GLY A 147 REMARK 465 VAL A 148 REMARK 465 ASN A 149 REMARK 465 ASN A 150 REMARK 465 GLY A 151 REMARK 465 ASN A 152 REMARK 465 PRO A 153 REMARK 465 LEU A 154 REMARK 465 ASP A 155 REMARK 465 ALA A 156 REMARK 465 VAL A 157 REMARK 465 GLN A 158 REMARK 465 GLN A 159 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 THR A 42 C THR A 42 O 0.124 REMARK 500 TYR A 83 CG TYR A 83 CD2 0.084 REMARK 500 TYR A 83 CG TYR A 83 CD1 0.078 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 THR A 28 CA - CB - CG2 ANGL. DEV. = 10.8 DEGREES REMARK 500 PHE A 29 CB - CA - C ANGL. DEV. = 14.1 DEGREES REMARK 500 SER A 52 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP A 61 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP A 79 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 ASN A 81 CB - CA - C ANGL. DEV. = 12.8 DEGREES 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 ALA A 46 -25.87 -28.39 REMARK 500 SER A 52 -147.03 75.68 REMARK 500 THR A 66 52.76 -103.49 REMARK 500 ASN A 81 -165.86 -125.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTN A 5100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31084 RELATED DB: EMDB REMARK 900 1.77 A CRYO-EM STRUCTURE OF STREPTAVIDIN USING FIRST 40 FRAMES REMARK 900 (CORRESPONDING TO ABOUT 40E/A^2 TOTAL DOSE) DBREF 7EFD A -23 159 UNP P22629 SAV_STRAV 1 183 SEQRES 1 A 183 MET ARG LYS ILE VAL VAL ALA ALA ILE ALA VAL SER LEU SEQRES 2 A 183 THR THR VAL SER ILE THR ALA SER ALA SER ALA ASP PRO SEQRES 3 A 183 SER LYS ASP SER LYS ALA GLN VAL SER ALA ALA GLU ALA SEQRES 4 A 183 GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SER THR SEQRES 5 A 183 PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU THR GLY SEQRES 6 A 183 THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER ARG TYR SEQRES 7 A 183 VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA THR ASP SEQRES 8 A 183 GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA TRP LYS SEQRES 9 A 183 ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR TRP SER SEQRES 10 A 183 GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE ASN THR SEQRES 11 A 183 GLN TRP LEU LEU THR SER GLY THR THR GLU ALA ASN ALA SEQRES 12 A 183 TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE THR LYS SEQRES 13 A 183 VAL LYS PRO SER ALA ALA SER ILE ASP ALA ALA LYS LYS SEQRES 14 A 183 ALA GLY VAL ASN ASN GLY ASN PRO LEU ASP ALA VAL GLN SEQRES 15 A 183 GLN HET BTN A5100 16 HETNAM BTN BIOTIN FORMUL 2 BTN C10 H16 N2 O3 S FORMUL 3 HOH *39(H2 O) HELIX 1 AA1 THR A 115 LYS A 121 5 7 SHEET 1 AA1 9 GLY A 19 ASN A 23 0 SHEET 2 AA1 9 THR A 28 ALA A 33 -1 O PHE A 29 N TRP A 21 SHEET 3 AA1 9 ALA A 38 GLU A 44 -1 O GLU A 44 N THR A 28 SHEET 4 AA1 9 ARG A 53 TYR A 60 -1 O GLY A 58 N LEU A 39 SHEET 5 AA1 9 THR A 71 LYS A 80 -1 O THR A 76 N THR A 57 SHEET 6 AA1 9 ASN A 85 VAL A 97 -1 O GLY A 94 N LEU A 73 SHEET 7 AA1 9 ARG A 103 SER A 112 -1 O ARG A 103 N VAL A 97 SHEET 8 AA1 9 THR A 123 THR A 131 -1 O ASP A 128 N THR A 106 SHEET 9 AA1 9 GLY A 19 ASN A 23 -1 N TYR A 22 O THR A 131 SITE 1 AC1 12 ASN A 23 SER A 27 TYR A 43 SER A 45 SITE 2 AC1 12 VAL A 47 GLY A 48 ASN A 49 TRP A 79 SITE 3 AC1 12 SER A 88 THR A 90 TRP A 108 ASP A 128 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 111.05100 MTRIX2 2 0.000000 -1.000000 0.000000 111.05100 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 MTRIX2 3 0.000000 -1.000000 0.000000 111.05100 MTRIX3 3 0.000000 0.000000 -1.000000 111.05100 MTRIX1 4 -1.000000 0.000000 0.000000 111.05100 MTRIX2 4 0.000000 1.000000 0.000000 0.00000 MTRIX3 4 0.000000 0.000000 -1.000000 111.05100