HEADER SUGAR BINDING PROTEIN 13-FEB-24 8YBE TITLE CRYO-EM STRUCTURE OF MALTOSE BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE/MALTODEXTRIN-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMBP,MALTODEXTRIN-BINDING PROTEIN,MALTOSE-BINDING PROTEIN, COMPND 5 MBP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MALE, B4034, JW3994; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MALTOSE BINDING PROTEIN, CRYO-EM, SUB-50KDA, ATOMIC RESOLUTION., KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.YOO,K.PARK,H.KIM REVDAT 2 02-JUL-25 8YBE 1 REMARK REVDAT 1 06-MAR-24 8YBE 0 JRNL AUTH Y.YOO,K.PARK,H.KIM JRNL TITL ATOMIC RESOLUTION STRUCTURE OF MBP USING CRYO-EM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.DUAN,J.A.HALL,H.NIKAIDO,F.A.QUIOCHO REMARK 1 TITL CRYSTAL STRUCTURES OF THE MALTODEXTRIN/MALTOSE-BINDING REMARK 1 TITL 2 PROTEIN COMPLEXED WITH REDUCED OLIGOSACCHARIDES: FLEXIBILITY REMARK 1 TITL 3 OF TERTIARY STRUCTURE AND LIGAND BINDING. REMARK 1 REF J MOL BIOL V. 306 1115 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11237621 REMARK 1 DOI 10.1006/JMBI.2001.4456 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, 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) : 2.300 REMARK 3 NUMBER OF PARTICLES : 517853 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 8YBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044681. 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 : MALTOSE BINDING PROTEIN MONOMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 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 : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39117 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MALTOSE BINDING PROTEIN DBREF 8YBE A 27 396 UNP P0AEX9 MALE_ECOLI 27 396 SEQADV 8YBE MET A 26 UNP P0AEX9 INITIATING METHIONINE SEQADV 8YBE VAL A 338 UNP P0AEX9 ALA 338 ENGINEERED MUTATION SEQRES 1 A 371 MET LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN SEQRES 2 A 371 GLY ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS SEQRES 3 A 371 LYS PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU SEQRES 4 A 371 HIS PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA SEQRES 5 A 371 ALA THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS SEQRES 6 A 371 ASP ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA SEQRES 7 A 371 GLU ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR SEQRES 8 A 371 PRO PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU SEQRES 9 A 371 ILE ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE SEQRES 10 A 371 TYR ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP SEQRES 11 A 371 GLU GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS SEQRES 12 A 371 GLY LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR SEQRES 13 A 371 PHE THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA SEQRES 14 A 371 PHE LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL SEQRES 15 A 371 GLY VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE SEQRES 16 A 371 LEU VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP SEQRES 17 A 371 THR ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY SEQRES 18 A 371 GLU THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER SEQRES 19 A 371 ASN ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL SEQRES 20 A 371 LEU PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL SEQRES 21 A 371 GLY VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN SEQRES 22 A 371 LYS GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU SEQRES 23 A 371 THR ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO SEQRES 24 A 371 LEU GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU SEQRES 25 A 371 VAL LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA SEQRES 26 A 371 GLN LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER SEQRES 27 A 371 ALA PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA SEQRES 28 A 371 ALA SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP SEQRES 29 A 371 ALA GLN THR ARG ILE THR LYS HET GLC B 1 12 HET GLC B 2 11 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 HOH *197(H2 O) HELIX 1 AA1 GLY A 42 GLY A 58 1 17 HELIX 2 AA2 LYS A 68 GLY A 80 1 13 HELIX 3 AA3 HIS A 90 GLY A 100 1 11 HELIX 4 AA4 ASP A 108 LEU A 115 1 8 HELIX 5 AA5 TYR A 116 VAL A 123 1 8 HELIX 6 AA6 GLU A 157 LYS A 168 1 12 HELIX 7 AA7 GLU A 179 ASP A 190 1 12 HELIX 8 AA8 ASN A 211 ASN A 227 1 17 HELIX 9 AA9 ASP A 235 LYS A 245 1 11 HELIX 10 AB1 GLY A 254 TRP A 256 5 3 HELIX 11 AB2 ALA A 257 LYS A 265 1 9 HELIX 12 AB3 ASN A 298 TYR A 309 1 12 HELIX 13 AB4 THR A 312 LYS A 323 1 12 HELIX 14 AB5 LEU A 330 VAL A 338 1 9 HELIX 15 AB6 ASP A 340 GLY A 353 1 14 HELIX 16 AB7 PRO A 360 GLY A 379 1 20 HELIX 17 AB8 THR A 382 LYS A 396 1 15 SHEET 1 AA1 6 LYS A 60 GLU A 64 0 SHEET 2 AA1 6 LYS A 32 TRP A 36 1 N ILE A 35 O GLU A 64 SHEET 3 AA1 6 ILE A 85 ALA A 89 1 O PHE A 87 N TRP A 36 SHEET 4 AA1 6 GLY A 286 ILE A 292 -1 O SER A 289 N TRP A 88 SHEET 5 AA1 6 TYR A 132 GLU A 137 -1 N GLU A 137 O GLY A 286 SHEET 6 AA1 6 ALA A 327 VAL A 328 -1 O ALA A 327 N VAL A 136 SHEET 1 AA2 2 ARG A 124 TYR A 125 0 SHEET 2 AA2 2 LYS A 128 LEU A 129 -1 O LYS A 128 N TYR A 125 SHEET 1 AA3 4 SER A 171 LEU A 173 0 SHEET 2 AA3 4 THR A 248 ASN A 253 1 O ALA A 249 N SER A 171 SHEET 3 AA3 4 SER A 140 ASN A 144 -1 N ASN A 144 O ALA A 249 SHEET 4 AA3 4 TYR A 268 THR A 271 -1 O THR A 271 N LEU A 141 SHEET 1 AA4 2 LYS A 196 GLU A 198 0 SHEET 2 AA4 2 LYS A 201 ASP A 203 -1 O ASP A 203 N LYS A 196 LINK O4 GLC B 1 C1 GLC B 2 1555 1555 1.43 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 CONECT 2892 2893 2898 2902 CONECT 2893 2892 2894 2899 CONECT 2894 2893 2895 2900 CONECT 2895 2894 2896 2901 CONECT 2896 2895 2897 2902 CONECT 2897 2896 2903 CONECT 2898 2892 CONECT 2899 2893 CONECT 2900 2894 CONECT 2901 2895 2904 CONECT 2902 2892 2896 CONECT 2903 2897 CONECT 2904 2901 2905 2913 CONECT 2905 2904 2906 2910 CONECT 2906 2905 2907 2911 CONECT 2907 2906 2908 2912 CONECT 2908 2907 2909 2913 CONECT 2909 2908 2914 CONECT 2910 2905 CONECT 2911 2906 CONECT 2912 2907 CONECT 2913 2904 2908 CONECT 2914 2909 MASTER 116 0 2 17 14 0 0 6 3099 1 23 29 END