HEADER SUGAR BINDING PROTEIN 13-FEB-26 28QN TITLE MBP-MALTOSE BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DARPIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MALTODEXTRIN-BINDING PROTEIN; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 8 ORGANISM_COMMON: METHANOSARCINA FRISIA; SOURCE 9 ORGANISM_TAXID: 2209; SOURCE 10 GENE: MALE, DU74_04045; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MBP, DARPIN, SCAFFOLD, SUGAR BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,M.FAIRHEAD,O.GITTINS,F.VON DELFT, AUTHOR 2 J.ENDICOTT,M.MARTIN,A.C.W.PIKE,D.B.SAUER,L.S.DLAMINI REVDAT 2 18-MAR-26 28QN 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQADV SEQRES HET HETNAM REVDAT 2 3 1 HETSYN FORMUL HELIX SHEET REVDAT 2 4 1 ATOM REVDAT 1 25-FEB-26 28QN 0 JRNL AUTH D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,O.GITTINS,M.MARTIN, JRNL AUTH 2 J.ENDICOTT,M.FAIRHEAD,F.VON DELFT,A.C.W.PIKE,D.B.SAUER, JRNL AUTH 3 L.S.DLAMINI JRNL TITL AN ENGINEERED SYMMETRICAL SCAFFOLD SYSTEM ENABLES HIGH JRNL TITL 2 RESOLUTION IMAGING OF SMALL CARGO PROTEINS BY CRYO-ELECTRON JRNL TITL 3 MICROSCOPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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 : 150405 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 28QN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1292153856. 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 : MBP BOUND TO DARPIN ON AN AHIR REMARK 245 DODECAMER SCAFFOLD SYSTEM.; REMARK 245 DARPIN; MBP 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 : 7.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 5050.00 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 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 ASP A 13 CG OD1 OD2 REMARK 470 LEU A 14 CG CD1 CD2 REMARK 470 ARG A 16 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 GLU A 20 CG CD OE1 OE2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 ASP A 27 CG OD1 OD2 REMARK 470 ASP A 28 CG OD1 OD2 REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 VAL A 30 CG1 CG2 REMARK 470 ARG A 31 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 32 CG1 CG2 CD1 REMARK 470 LEU A 33 CG CD1 CD2 REMARK 470 MET A 34 CG SD CE REMARK 470 ASN A 36 CG OD1 ND2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU C 112 O2 GLC B 1 2.11 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 GLU A 29 -119.67 -125.94 REMARK 500 GLU A 29 -119.67 -125.94 REMARK 500 VAL A 30 -114.68 27.72 REMARK 500 VAL A 30 -114.68 27.72 REMARK 500 ILE C 109 -56.64 -122.50 REMARK 500 ALA C 169 -7.62 72.34 REMARK 500 ASN C 174 54.46 39.82 REMARK 500 ASP C 208 35.50 -100.00 REMARK 500 PRO C 335 3.28 -67.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-56751 RELATED DB: EMDB REMARK 900 MBP-MALTOSE BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) DBREF 28QN A 12 171 PDB 28QN 28QN 12 171 DBREF1 28QN C 1 374 UNP A0A0F8NYV9_METMZ DBREF2 28QN C A0A0F8NYV9 1 374 SEQADV 28QN ILE C 3 UNP A0A0F8NYV THR 3 CONFLICT SEQADV 28QN GLN C 4 UNP A0A0F8NYV GLU 4 CONFLICT SEQADV 28QN GLY C 369 UNP A0A0F8NYV SER 369 CONFLICT SEQADV 28QN HIS C 371 UNP A0A0F8NYV SER 371 CONFLICT SEQADV 28QN HIS C 372 UNP A0A0F8NYV ASN 372 CONFLICT SEQADV 28QN HIS C 373 UNP A0A0F8NYV ASN 373 CONFLICT SEQADV 28QN HIS C 374 UNP A0A0F8NYV ASN 374 CONFLICT SEQRES 1 A 160 ALA ASP LEU GLY ARG LYS LEU LEU GLU ALA ALA ARG ALA SEQRES 2 A 160 GLY GLN ASP ASP GLU VAL ARG ILE LEU MET ALA ASN GLY SEQRES 3 A 160 ALA ASP VAL ASN ALA ALA ASP ASN THR GLY THR THR PRO SEQRES 4 A 160 LEU HIS LEU ALA ALA TYR SER GLY HIS LEU GLU ILE VAL SEQRES 5 A 160 GLU VAL LEU LEU LYS HIS GLY ALA ASP VAL ASP ALA SER SEQRES 6 A 160 ASP VAL PHE GLY TYR THR PRO LEU HIS LEU ALA ALA TYR SEQRES 7 A 160 TRP GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS ASN SEQRES 8 A 160 GLY ALA ASP VAL ASN ALA MET ASP SER ASP GLY MET THR SEQRES 9 A 160 PRO LEU HIS LEU ALA ALA LYS TRP GLY TYR LEU GLU ILE SEQRES 10 A 160 VAL GLU VAL LEU LEU LYS HIS GLY ALA ASP VAL ASN ALA SEQRES 11 A 160 GLN ASP LYS PHE GLY LYS THR PRO LYS ASP LEU ALA ARG SEQRES 12 A 160 ASP ASN GLY ASN GLN TRP ILE TYR GLU LEU LEU GLU ALA SEQRES 13 A 160 ALA GLY ARG ALA SEQRES 1 C 374 MET LYS ILE GLN GLU GLY LYS LEU VAL ILE TRP ILE ASN SEQRES 2 C 374 GLY ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS SEQRES 3 C 374 LYS PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU SEQRES 4 C 374 HIS PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA SEQRES 5 C 374 ALA THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS SEQRES 6 C 374 ASP ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA SEQRES 7 C 374 GLU ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR SEQRES 8 C 374 PRO PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU SEQRES 9 C 374 ILE ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE SEQRES 10 C 374 TYR ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP SEQRES 11 C 374 GLU GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS SEQRES 12 C 374 GLY LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR SEQRES 13 C 374 PHE THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA SEQRES 14 C 374 PHE LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL SEQRES 15 C 374 GLY VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE SEQRES 16 C 374 LEU VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP SEQRES 17 C 374 THR ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY SEQRES 18 C 374 GLU THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER SEQRES 19 C 374 ASN ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL SEQRES 20 C 374 LEU PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL SEQRES 21 C 374 GLY VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN SEQRES 22 C 374 LYS GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU SEQRES 23 C 374 THR ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO SEQRES 24 C 374 LEU GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU SEQRES 25 C 374 ALA LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA SEQRES 26 C 374 GLN LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER SEQRES 27 C 374 ALA PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA SEQRES 28 C 374 ALA SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP SEQRES 29 C 374 ALA GLN THR ASN GLY SER HIS HIS HIS HIS HET GLC B 1 12 HET GLC B 2 11 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 GLC 2(C6 H12 O6) HELIX 1 AA1 ALA A 12 ALA A 24 1 13 HELIX 2 AA2 GLU A 29 ALA A 35 1 7 HELIX 3 AA3 THR A 49 GLY A 58 1 10 HELIX 4 AA4 HIS A 59 HIS A 69 1 11 HELIX 5 AA5 THR A 82 TRP A 90 1 9 HELIX 6 AA6 HIS A 92 GLY A 103 1 12 HELIX 7 AA7 THR A 115 TRP A 123 1 9 HELIX 8 AA8 TYR A 125 HIS A 135 1 11 HELIX 9 AA9 THR A 148 GLY A 157 1 10 HELIX 10 AB1 ASN A 158 LEU A 165 1 8 HELIX 11 AB2 GLU A 166 ALA A 171 1 6 HELIX 12 AB3 GLY C 17 THR C 32 1 16 HELIX 13 AB4 LYS C 43 GLY C 55 1 13 HELIX 14 AB5 ARG C 67 SER C 74 1 8 HELIX 15 AB6 ASP C 83 LEU C 90 1 8 HELIX 16 AB7 TYR C 91 ALA C 97 1 7 HELIX 17 AB8 GLU C 131 LYS C 143 1 13 HELIX 18 AB9 GLU C 154 ALA C 164 1 11 HELIX 19 AC1 ASN C 186 ASN C 202 1 17 HELIX 20 AC2 ASP C 210 LYS C 220 1 11 HELIX 21 AC3 GLY C 229 TRP C 231 5 3 HELIX 22 AC4 ALA C 232 LYS C 240 1 9 HELIX 23 AC5 ASN C 273 TYR C 284 1 12 HELIX 24 AC6 THR C 287 LYS C 298 1 12 HELIX 25 AC7 LEU C 305 ALA C 313 1 9 HELIX 26 AC8 ASP C 315 GLY C 328 1 14 HELIX 27 AC9 GLN C 336 GLY C 354 1 19 HELIX 28 AD1 THR C 357 HIS C 371 1 15 SHEET 1 AA1 5 VAL C 36 GLU C 39 0 SHEET 2 AA1 5 LEU C 8 TRP C 11 1 N ILE C 10 O THR C 37 SHEET 3 AA1 5 ILE C 60 ALA C 64 1 O PHE C 62 N TRP C 11 SHEET 4 AA1 5 PHE C 259 ILE C 267 -1 O SER C 264 N TRP C 63 SHEET 5 AA1 5 TYR C 107 GLU C 112 -1 N GLU C 112 O GLY C 261 SHEET 1 AA2 5 VAL C 36 GLU C 39 0 SHEET 2 AA2 5 LEU C 8 TRP C 11 1 N ILE C 10 O THR C 37 SHEET 3 AA2 5 ILE C 60 ALA C 64 1 O PHE C 62 N TRP C 11 SHEET 4 AA2 5 PHE C 259 ILE C 267 -1 O SER C 264 N TRP C 63 SHEET 5 AA2 5 GLU C 329 ILE C 330 1 O GLU C 329 N VAL C 260 SHEET 1 AA3 2 ARG C 99 TYR C 100 0 SHEET 2 AA3 2 LYS C 103 LEU C 104 -1 O LYS C 103 N TYR C 100 SHEET 1 AA4 4 SER C 146 LEU C 148 0 SHEET 2 AA4 4 THR C 223 ASN C 228 1 O MET C 225 N ALA C 147 SHEET 3 AA4 4 SER C 115 ASN C 119 -1 N ASN C 119 O ALA C 224 SHEET 4 AA4 4 TYR C 243 THR C 246 -1 O GLY C 244 N TYR C 118 SHEET 1 AA5 2 LYS C 171 TYR C 172 0 SHEET 2 AA5 2 TYR C 177 ASP C 178 -1 O ASP C 178 N LYS C 171 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 4064 4065 4070 4074 CONECT 4065 4064 4066 4071 CONECT 4066 4065 4067 4072 CONECT 4067 4066 4068 4073 CONECT 4068 4067 4069 4074 CONECT 4069 4068 4075 CONECT 4070 4064 CONECT 4071 4065 CONECT 4072 4066 CONECT 4073 4067 4076 CONECT 4074 4064 4068 CONECT 4075 4069 CONECT 4076 4073 4077 4085 CONECT 4077 4076 4078 4082 CONECT 4078 4077 4079 4083 CONECT 4079 4078 4080 4084 CONECT 4080 4079 4081 4085 CONECT 4081 4080 4086 CONECT 4082 4077 CONECT 4083 4078 CONECT 4084 4079 CONECT 4085 4076 4080 CONECT 4086 4081 MASTER 162 0 2 28 18 0 0 6 4076 2 23 42 END