HEADER TRANSPORT PROTEIN 25-MAR-22 7UGX TITLE ASP-BOUND GLTPH RSMR MUTANT IN IFS-B1 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE TRANSPORTER HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLT(PH),SODIUM-ASPARTATE SYMPORTER GLT(PH),SODIUM-DEPENDENT COMPND 5 ASPARTATE TRANSPORTER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 GENE: PH1295; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLTPH, GLUTAMATE TRANSPORTER, SUBSTRATE, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.HUANG,O.BOUDKER REVDAT 2 10-MAY-23 7UGX 1 JRNL REVDAT 1 29-MAR-23 7UGX 0 JRNL AUTH Y.HUANG,K.D.REDDY,C.BRACKEN,B.QIU,W.ZHAN,D.ELIEZER,O.BOUDKER JRNL TITL ENVIRONMENTALLY ULTRASENSITIVE FLUORINE PROBE TO RESOLVE JRNL TITL 2 PROTEIN CONFORMATIONAL ENSEMBLES BY 19 F NMR AND CRYO-EM. JRNL REF J.AM.CHEM.SOC. V. 145 8583 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37023263 JRNL DOI 10.1021/JACS.3C01003 REMARK 2 REMARK 2 RESOLUTION. 2.96 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) : 2.960 REMARK 3 NUMBER OF PARTICLES : 326008 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7UGX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000264174. 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 : GLTPH RSMR MUTANT BOUND WITH NA REMARK 245 AND ASP 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 : 7.40 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 5094.00 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 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 1 REMARK 465 GLY A 417 REMARK 465 THR A 418 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 VAL A 222 -67.01 61.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 89 O REMARK 620 2 THR A 92 OG1 68.6 REMARK 620 3 SER A 93 OG 66.5 121.9 REMARK 620 4 ASN A 310 OD1 117.2 102.5 130.0 REMARK 620 5 ASP A 312 OD1 133.8 92.9 92.7 107.8 REMARK 620 6 ASP A 312 OD2 151.9 83.3 134.2 67.3 44.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 306 O REMARK 620 2 ASN A 310 O 100.8 REMARK 620 3 ASN A 401 O 145.6 75.9 REMARK 620 4 ASP A 405 OD1 68.2 85.8 77.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 308 O REMARK 620 2 SER A 349 O 117.2 REMARK 620 3 ILE A 350 O 82.0 81.7 REMARK 620 4 THR A 352 O 111.5 119.2 71.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26498 RELATED DB: EMDB REMARK 900 ASP-BOUND GLTPH RSMR MUTANT IN IFS STATE DBREF 7UGX A 1 418 UNP O59010 GLT_PYRHO 1 418 SEQADV 7UGX HIS A 37 UNP O59010 ASP 37 ENGINEERED MUTATION SEQADV 7UGX HIS A 40 UNP O59010 LYS 40 ENGINEERED MUTATION SEQADV 7UGX HIS A 125 UNP O59010 LYS 125 ENGINEERED MUTATION SEQADV 7UGX HIS A 132 UNP O59010 LYS 132 ENGINEERED MUTATION SEQADV 7UGX HIS A 215 UNP O59010 TYR 215 ENGINEERED MUTATION SEQADV 7UGX HIS A 219 UNP O59010 GLU 219 ENGINEERED MUTATION SEQADV 7UGX HIS A 223 UNP O59010 LYS 223 ENGINEERED MUTATION SEQADV 7UGX HIS A 264 UNP O59010 LYS 264 ENGINEERED MUTATION SEQADV 7UGX SER A 276 UNP O59010 ARG 276 ENGINEERED MUTATION SEQADV 7UGX ALA A 321 UNP O59010 CYS 321 ENGINEERED MUTATION SEQADV 7UGX HIS A 368 UNP O59010 GLU 368 ENGINEERED MUTATION SEQADV 7UGX EFC A 385 UNP O59010 MET 385 ENGINEERED MUTATION SEQADV 7UGX ARG A 395 UNP O59010 MET 395 ENGINEERED MUTATION SEQADV 7UGX THR A 418 UNP O59010 GLU 418 ENGINEERED MUTATION SEQRES 1 A 418 MET GLY LEU TYR ARG LYS TYR ILE GLU TYR PRO VAL LEU SEQRES 2 A 418 GLN LYS ILE LEU ILE GLY LEU ILE LEU GLY ALA ILE VAL SEQRES 3 A 418 GLY LEU ILE LEU GLY HIS TYR GLY TYR ALA HIS ALA VAL SEQRES 4 A 418 HIS THR TYR VAL LYS PRO PHE GLY ASP LEU PHE VAL ARG SEQRES 5 A 418 LEU LEU LYS MET LEU VAL MET PRO ILE VAL PHE ALA SER SEQRES 6 A 418 LEU VAL VAL GLY ALA ALA SER ILE SER PRO ALA ARG LEU SEQRES 7 A 418 GLY ARG VAL GLY VAL LYS ILE VAL VAL TYR TYR LEU LEU SEQRES 8 A 418 THR SER ALA PHE ALA VAL THR LEU GLY ILE ILE MET ALA SEQRES 9 A 418 ARG LEU PHE ASN PRO GLY ALA GLY ILE HIS LEU ALA VAL SEQRES 10 A 418 GLY GLY GLN GLN PHE GLN PRO HIS GLN ALA PRO PRO LEU SEQRES 11 A 418 VAL HIS ILE LEU LEU ASP ILE VAL PRO THR ASN PRO PHE SEQRES 12 A 418 GLY ALA LEU ALA ASN GLY GLN VAL LEU PRO THR ILE PHE SEQRES 13 A 418 PHE ALA ILE ILE LEU GLY ILE ALA ILE THR TYR LEU MET SEQRES 14 A 418 ASN SER GLU ASN GLU LYS VAL ARG LYS SER ALA GLU THR SEQRES 15 A 418 LEU LEU ASP ALA ILE ASN GLY LEU ALA GLU ALA MET TYR SEQRES 16 A 418 LYS ILE VAL ASN GLY VAL MET GLN TYR ALA PRO ILE GLY SEQRES 17 A 418 VAL PHE ALA LEU ILE ALA HIS VAL MET ALA HIS GLN GLY SEQRES 18 A 418 VAL HIS VAL VAL GLY GLU LEU ALA LYS VAL THR ALA ALA SEQRES 19 A 418 VAL TYR VAL GLY LEU THR LEU GLN ILE LEU LEU VAL TYR SEQRES 20 A 418 PHE VAL LEU LEU LYS ILE TYR GLY ILE ASP PRO ILE SER SEQRES 21 A 418 PHE ILE LYS HIS ALA LYS ASP ALA MET LEU THR ALA PHE SEQRES 22 A 418 VAL THR SER SER SER SER GLY THR LEU PRO VAL THR MET SEQRES 23 A 418 ARG VAL ALA LYS GLU MET GLY ILE SER GLU GLY ILE TYR SEQRES 24 A 418 SER PHE THR LEU PRO LEU GLY ALA THR ILE ASN MET ASP SEQRES 25 A 418 GLY THR ALA LEU TYR GLN GLY VAL ALA THR PHE PHE ILE SEQRES 26 A 418 ALA ASN ALA LEU GLY SER HIS LEU THR VAL GLY GLN GLN SEQRES 27 A 418 LEU THR ILE VAL LEU THR ALA VAL LEU ALA SER ILE GLY SEQRES 28 A 418 THR ALA GLY VAL PRO GLY ALA GLY ALA ILE MET LEU ALA SEQRES 29 A 418 MET VAL LEU HIS SER VAL GLY LEU PRO LEU THR ASP PRO SEQRES 30 A 418 ASN VAL ALA ALA ALA TYR ALA EFC ILE LEU GLY ILE ASP SEQRES 31 A 418 ALA ILE LEU ASP ARG GLY ARG THR MET VAL ASN VAL THR SEQRES 32 A 418 GLY ASP LEU THR GLY THR ALA ILE VAL ALA LYS THR GLU SEQRES 33 A 418 GLY THR HET EFC A 385 10 HET ASP A 501 9 HET NA A 502 1 HET NA A 503 1 HET NA A 504 1 HETNAM EFC S,S-(2-FLUOROETHYL)THIOCYSTEINE HETNAM ASP ASPARTIC ACID HETNAM NA SODIUM ION FORMUL 1 EFC C5 H10 F N O2 S2 FORMUL 2 ASP C4 H7 N O4 FORMUL 3 NA 3(NA 1+) HELIX 1 AA1 GLY A 2 GLU A 9 1 8 HELIX 2 AA2 PRO A 11 TYR A 33 1 23 HELIX 3 AA3 TYR A 35 VAL A 43 1 9 HELIX 4 AA4 VAL A 43 LEU A 57 1 15 HELIX 5 AA5 LEU A 57 ILE A 73 1 17 HELIX 6 AA6 VAL A 81 PHE A 107 1 27 HELIX 7 AA7 ALA A 116 GLN A 120 5 5 HELIX 8 AA8 PRO A 129 ASP A 136 1 8 HELIX 9 AA9 ASN A 141 ASN A 148 1 8 HELIX 10 AB1 GLN A 150 ASN A 170 1 21 HELIX 11 AB2 ASN A 173 GLN A 220 1 48 HELIX 12 AB3 VAL A 222 VAL A 246 1 25 HELIX 13 AB4 VAL A 246 GLY A 255 1 10 HELIX 14 AB5 ASP A 257 ALA A 265 1 9 HELIX 15 AB6 ALA A 265 SER A 276 1 12 HELIX 16 AB7 THR A 281 GLU A 291 1 11 HELIX 17 AB8 SER A 295 THR A 308 1 14 HELIX 18 AB9 MET A 311 GLY A 330 1 20 HELIX 19 AC1 THR A 334 THR A 352 1 19 HELIX 20 AC2 GLY A 357 GLY A 371 1 15 HELIX 21 AC3 ASP A 376 ILE A 389 1 14 HELIX 22 AC4 ILE A 389 THR A 415 1 27 LINK C ALA A 384 N EFC A 385 1555 1555 1.33 LINK C EFC A 385 N ILE A 386 1555 1555 1.33 LINK O TYR A 89 NA NA A 504 1555 1555 2.63 LINK OG1 THR A 92 NA NA A 504 1555 1555 2.47 LINK OG SER A 93 NA NA A 504 1555 1555 2.46 LINK O GLY A 306 NA NA A 502 1555 1555 2.66 LINK O THR A 308 NA NA A 503 1555 1555 2.43 LINK O ASN A 310 NA NA A 502 1555 1555 2.86 LINK OD1 ASN A 310 NA NA A 504 1555 1555 2.49 LINK OD1 ASP A 312 NA NA A 504 1555 1555 2.51 LINK OD2 ASP A 312 NA NA A 504 1555 1555 3.07 LINK O SER A 349 NA NA A 503 1555 1555 2.23 LINK O ILE A 350 NA NA A 503 1555 1555 3.11 LINK O THR A 352 NA NA A 503 1555 1555 2.65 LINK O ASN A 401 NA NA A 502 1555 1555 2.93 LINK OD1 ASP A 405 NA NA A 502 1555 1555 2.66 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