HEADER PROTEIN BINDING 09-OCT-24 9H1N TITLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE (E2) PSBD IN COMPLEX WITH THE TITLE 2 PYRUVATE DEHYDROGENASE (E1) BINDING DOMAIN FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE E1 COMPONENT; COMPND 3 CHAIN: C, B; COMPND 4 SYNONYM: PDH E1 COMPONENT; COMPND 5 EC: 1.2.4.1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ISOLATED BINDING DOMAIN OF E1 (RESIDUES 1-50); COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF COMPND 10 PYRUVATE DEHYDROGENASE COMPLEX; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE (E2) COMPONENT COMPND 13 OF PYRUVATE DEHYDROGENASE COMPLEX; COMPND 14 EC: 2.3.1.12; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ACEE, B0114, JW0110; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 GENE: ACEF, B0115, JW0111; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, PYRUVATE DEHYDROGENASE, OXIDOREDUCTASE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.N.BOTHE,D.RACUNICA,R.GLOCKSHUBER REVDAT 1 29-OCT-25 9H1N 0 JRNL AUTH S.N.BOTHE,D.RACUNICA,T.ZAJEC HUDNIK,R.ZDANOWICZ,A.BOTHE, JRNL AUTH 2 C.GIESE,R.GLOCKSHUBER JRNL TITL A COOPERATIVE BINDING MECHANISM STEERS THE RECRUITMENT OF JRNL TITL 2 PERIPHERAL SUBUNITS IN THE E. COLI PYRUVATE DEHYDROGENASE JRNL TITL 3 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24522 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.0200 - 3.2100 1.00 2780 133 0.1789 0.1829 REMARK 3 2 3.2100 - 2.5500 1.00 2639 137 0.2113 0.2406 REMARK 3 3 2.5500 - 2.2300 1.00 2602 132 0.2072 0.2565 REMARK 3 4 2.2300 - 2.0200 1.00 2542 156 0.2096 0.2253 REMARK 3 5 2.0200 - 1.8800 1.00 2562 151 0.2430 0.3042 REMARK 3 6 1.8800 - 1.7700 1.00 2533 136 0.2533 0.3014 REMARK 3 7 1.7700 - 1.6800 1.00 2578 116 0.2610 0.3077 REMARK 3 8 1.6800 - 1.6100 1.00 2545 141 0.3099 0.3245 REMARK 3 9 1.6100 - 1.5400 0.99 2526 113 0.3824 0.3803 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.224 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.956 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 1239 REMARK 3 ANGLE : 1.236 1679 REMARK 3 CHIRALITY : 0.079 185 REMARK 3 PLANARITY : 0.011 227 REMARK 3 DIHEDRAL : 4.190 179 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9H1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24525 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 39.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01196 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.61790 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 56% TACSIMATE PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.17050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.63100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.63100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.58525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.63100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.63100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.75575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.63100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.63100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 10.58525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.63100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.63100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.75575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 21.17050 REMARK 290 REMARK 290 REMARK: NULL 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, B, 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 APPLY THE FOLLOWING TO CHAINS: C, B, A REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -21.17050 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 115 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 120 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 129 LIES ON A SPECIAL POSITION. 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 SER C 1 REMARK 465 GLU C 2 REMARK 465 ARG C 3 REMARK 465 SER B 1 REMARK 465 GLU B 2 REMARK 465 GLU A 314 REMARK 465 GLY A 315 REMARK 465 LYS A 316 REMARK 465 SER A 317 REMARK 465 GLU A 318 REMARK 465 PHE A 319 REMARK 465 PRO A 375 REMARK 465 ALA A 376 REMARK 465 ALA A 377 REMARK 465 THR A 378 REMARK 465 GLY A 379 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 120 O HOH A 460 3455 2.18 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 ASP C 9 77.24 -155.14 REMARK 500 ASP B 7 110.12 -39.21 REMARK 500 ASP B 9 77.59 -154.13 REMARK 500 GLU A 372 4.17 -68.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 9H1N C 1 49 UNP P0AFG8 ODP1_ECOLI 2 50 DBREF 9H1N B 1 49 UNP P0AFG8 ODP1_ECOLI 2 50 DBREF 9H1N A 314 379 UNP P06959 ODP2_ECOLI 315 380 SEQRES 1 C 49 SER GLU ARG PHE PRO ASN ASP VAL ASP PRO ILE GLU THR SEQRES 2 C 49 ARG ASP TRP LEU GLN ALA ILE GLU SER VAL ILE ARG GLU SEQRES 3 C 49 GLU GLY VAL GLU ARG ALA GLN TYR LEU ILE ASP GLN LEU SEQRES 4 C 49 LEU ALA GLU ALA ARG LYS GLY GLY VAL ASN SEQRES 1 B 49 SER GLU ARG PHE PRO ASN ASP VAL ASP PRO ILE GLU THR SEQRES 2 B 49 ARG ASP TRP LEU GLN ALA ILE GLU SER VAL ILE ARG GLU SEQRES 3 B 49 GLU GLY VAL GLU ARG ALA GLN TYR LEU ILE ASP GLN LEU SEQRES 4 B 49 LEU ALA GLU ALA ARG LYS GLY GLY VAL ASN SEQRES 1 A 66 GLU GLY LYS SER GLU PHE ALA GLU ASN ASP ALA TYR VAL SEQRES 2 A 66 HIS ALA THR PRO LEU ILE ARG ARG LEU ALA ARG GLU PHE SEQRES 3 A 66 GLY VAL ASN LEU ALA LYS VAL LYS GLY THR GLY ARG LYS SEQRES 4 A 66 GLY ARG ILE LEU ARG GLU ASP VAL GLN ALA TYR VAL LYS SEQRES 5 A 66 GLU ALA ILE LYS ARG ALA GLU ALA ALA PRO ALA ALA THR SEQRES 6 A 66 GLY FORMUL 4 HOH *122(H2 O) HELIX 1 AA1 ASP C 9 GLY C 28 1 20 HELIX 2 AA2 GLY C 28 GLY C 47 1 20 HELIX 3 AA3 ASP B 9 GLY B 28 1 20 HELIX 4 AA4 GLY B 28 GLY B 46 1 19 HELIX 5 AA5 GLU A 321 TYR A 325 5 5 HELIX 6 AA6 THR A 329 GLY A 340 1 12 HELIX 7 AA7 ASN A 342 VAL A 346 5 5 HELIX 8 AA8 GLY A 350 ARG A 354 5 5 HELIX 9 AA9 LEU A 356 GLU A 372 1 17 CRYST1 87.262 87.262 42.341 90.00 90.00 90.00 P 41 21 2 16 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 0.011460 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023618 0.00000 MASTER 288 0 0 9 0 0 0 6 1304 3 0 14 END