HEADER CHAPERONE 22-APR-26 25YC TITLE PSEUDOMONAS AERUGINOSA ACHC2 (YFDX2) AT PH 7.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: YFDX PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C-TERM: EXPRESSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: TUEID40_02116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.JUNG,S.S.CHA REVDAT 1 04-NOV-26 25YC 0 JRNL AUTH S.HAM,Y.J.JUNG,H.KIM,S.S.CHA,C.LEE JRNL TITL PH-DRIVEN TWO-STAGE CONFORMATIONAL SWITCHING ACTIVATES AN JRNL TITL 2 ACID-RESPONSIVE CHAPERONE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. 64206 2026 JRNL REFN ESSN 1521-3773 JRNL PMID 42891937 JRNL DOI 10.1002/ANIE.7464206 REMARK 2 REMARK 2 RESOLUTION. 2.48 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.590 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 18747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1868 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 32.1000 - 5.8100 0.95 1299 145 0.1976 0.2296 REMARK 3 2 5.8100 - 4.6200 1.00 1323 141 0.1875 0.2053 REMARK 3 3 4.6200 - 4.0400 1.00 1312 149 0.1809 0.1986 REMARK 3 4 4.0300 - 3.6700 1.00 1314 146 0.2102 0.2210 REMARK 3 5 3.6700 - 3.4000 1.00 1309 143 0.2298 0.2847 REMARK 3 6 3.4000 - 3.2000 1.00 1294 147 0.2364 0.3050 REMARK 3 7 3.2000 - 3.0400 1.00 1303 141 0.2751 0.3131 REMARK 3 8 3.0400 - 2.9100 1.00 1304 141 0.2884 0.3180 REMARK 3 9 2.9100 - 2.8000 1.00 1299 142 0.2767 0.3085 REMARK 3 10 2.8000 - 2.7000 1.00 1302 140 0.2654 0.2976 REMARK 3 11 2.7000 - 2.6200 1.00 1284 147 0.2862 0.2633 REMARK 3 12 2.6200 - 2.5400 1.00 1307 148 0.2743 0.3238 REMARK 3 13 2.5400 - 2.4800 0.96 1229 138 0.3161 0.3199 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) : 0.327 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.58 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 : 0.003 2145 REMARK 3 ANGLE : 0.614 2907 REMARK 3 CHIRALITY : 0.040 356 REMARK 3 PLANARITY : 0.006 374 REMARK 3 DIHEDRAL : 13.700 810 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 25YC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-26. REMARK 100 THE DEPOSITION ID IS D_1300073378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97948 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOXDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 32.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 69.4720 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 69.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M SODIUM/POTASSIUM PHOSPHATE PH7.0, REMARK 280 MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-Z 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.17633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.35267 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 74.35267 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.17633 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 -90.67000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 37.17633 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 ASN A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 ASN A 7 REMARK 465 PRO A 8 REMARK 465 ASN A 9 REMARK 465 ALA A 10 REMARK 465 THR A 11 REMARK 465 ASN A 12 REMARK 465 GLU A 13 REMARK 465 GLY A 14 REMARK 465 ILE A 15 REMARK 465 ASN A 16 REMARK 465 GLU A 17 REMARK 465 GLN A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 VAL A 21 REMARK 465 SER A 22 REMARK 465 HIS A 303 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 GLU A 229 CG CD OE1 OE2 REMARK 470 GLU A 297 CG CD OE1 OE2 REMARK 470 HIS A 302 CG ND1 CD2 CE1 NE2 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 LEU A 24 -38.04 171.37 REMARK 500 VAL A 26 168.98 66.20 REMARK 500 SER A 27 -178.55 -60.71 REMARK 500 PRO A 28 160.36 -47.39 REMARK 500 SER A 30 113.03 69.26 REMARK 500 ASP A 79 73.95 -151.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 25YC A 1 303 PDB 25YC 25YC 1 303 SEQRES 1 A 303 MET ASN GLU GLN THR PRO ASN PRO ASN ALA THR ASN GLU SEQRES 2 A 303 GLY ILE ASN GLU GLN ALA ALA VAL SER SER LEU PRO VAL SEQRES 3 A 303 SER PRO GLU SER LYS PRO GLU VAL VAL THR GLU VAL GLN SEQRES 4 A 303 PRO GLU VAL GLN LYS GLU THR ASP SER GLN ALA ALA ASP SEQRES 5 A 303 LYS ARG LYS GLN VAL LEU ASP GLU ALA VAL SER ALA LEU SEQRES 6 A 303 ALA LEU THR LYS SER ALA LEU ALA ALA LEU ASP GLY LYS SEQRES 7 A 303 ASP ALA ALA ARG ALA LEU ALA THR LEU ALA GLU VAL THR SEQRES 8 A 303 GLY LYS LEU GLU LEU ILE VAL ALA ARG GLU PRO THR LEU SEQRES 9 A 303 ALA LEU ALA PRO VAL ASP VAL ARG THR ILE VAL HIS ASP SEQRES 10 A 303 LEU PHE ALA ASN THR GLU THR ILE GLU ALA MET THR ASP SEQRES 11 A 303 GLU ALA LEU ASP ALA LEU LYS HIS GLY GLU VAL GLN GLN SEQRES 12 A 303 ALA ARG HIS VAL LEU ALA LEU LEU ALA SER GLU ILE VAL SEQRES 13 A 303 ILE ALA VAL THR ASN ILE PRO LEU ALA SER TYR PRO ALA SEQRES 14 A 303 ALA VAL LYS SER VAL VAL PRO LEU ILE ASP GLN GLY LYS SEQRES 15 A 303 ILE GLU GLU ALA LYS ALA ALA LEU GLN ALA ALA LEU SER SEQRES 16 A 303 THR LEU VAL GLU THR ARG SER VAL HIS PRO LEU PRO ALA SEQRES 17 A 303 LEU ARG ALA ARG LEU LEU LEU LYS ARG ALA GLU THR LEU SEQRES 18 A 303 VAL GLU ASP GLY GLN ARG SER GLU ALA SER ASN GLU ARG SEQRES 19 A 303 LEU GLU THR LEU LEU ASN GLU ALA ARG GLN GLN LEU GLU SEQRES 20 A 303 MET ALA GLU LEU LEU GLY TYR GLY LYS LYS LYS ASP PHE SEQRES 21 A 303 GLU PRO LEU TYR ALA GLU LEU LYS LYS VAL LYS GLN LYS SEQRES 22 A 303 THR ALA GLY GLY GLY GLY GLY LYS GLY TRP LEU ASP GLU SEQRES 23 A 303 ILE LYS ALA LYS LEU SER LYS LEU PHE LEU GLU HIS HIS SEQRES 24 A 303 HIS HIS HIS HIS HELIX 1 AA1 PRO A 32 VAL A 38 1 7 HELIX 2 AA2 VAL A 38 GLN A 56 1 19 HELIX 3 AA3 LEU A 58 GLY A 77 1 20 HELIX 4 AA4 ASP A 79 GLU A 101 1 23 HELIX 5 AA5 ASN A 121 HIS A 138 1 18 HELIX 6 AA6 GLU A 140 ALA A 149 1 10 HELIX 7 AA7 SER A 166 SER A 173 1 8 HELIX 8 AA8 SER A 173 GLN A 180 1 8 HELIX 9 AA9 LYS A 182 SER A 195 1 14 HELIX 10 AB1 LEU A 206 GLU A 223 1 18 HELIX 11 AB2 SER A 228 LEU A 252 1 25 HELIX 12 AB3 LYS A 256 LYS A 258 5 3 HELIX 13 AB4 ASP A 259 THR A 274 1 16 HELIX 14 AB5 ALA A 275 GLY A 278 5 4 HELIX 15 AB6 LEU A 284 PHE A 295 1 12 SHEET 1 AA1 3 LEU A 106 HIS A 116 0 SHEET 2 AA1 3 GLU A 154 PRO A 163 -1 O THR A 160 N VAL A 109 SHEET 3 AA1 3 VAL A 198 PRO A 205 -1 O THR A 200 N VAL A 159 CRYST1 90.670 90.670 111.529 90.00 90.00 120.00 P 31 1 2 6 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 0.011029 0.006368 0.000000 0.00000 SCALE2 0.000000 0.012735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008966 0.00000 MASTER 277 0 0 15 3 0 0 6 2118 1 0 24 END