HEADER DE NOVO PROTEIN 02-JUL-25 9VP8 TITLE CRYSTAL STRUCTURE OF YDJB FROM SALMONELLA ENTERICA SUBSP. ENTERICA TITLE 2 SEROVAR TYPHI COMPND MOL_ID: 1; COMPND 2 MOLECULE: YDJB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMINO ACID-BINDING PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA; SOURCE 3 ORGANISM_TAXID: 59201; SOURCE 4 GENE: CQE41_24605, CQE41_26710, D4Z17_24465, D4Z17_25245, SOURCE 5 DO679_24685, DO679_25805, DTU87_24435, DTU87_24900, E0U76_23790, SOURCE 6 E0U76_24960, EHB73_24130, EHB73_25360, EUC09_23745, EUC09_25055, SOURCE 7 EZX96_24135, EZX96_25275, F3E63_24010, F3E63_25325, F9Q85_23760, SOURCE 8 F9X98_23685, F9X98_24595, FE718_22725, FE718_24365, FQS30_23565, SOURCE 9 FQS30_24460, G1G93_23595, G1G93_23875, G1H47_23580, G1H47_23880, SOURCE 10 G1H91_23595, G1H91_23880, G1I18_23580, G1I18_23860, G2927_23595, SOURCE 11 G2927_24200, G3A19_23495, G3A19_24225, G3A20_08050, G3A20_24365, SOURCE 12 GB022_24295, GB022_24500, GB054_22795, GB054_24050, GB132_23520, SOURCE 13 GB151_24070, GB151_25030, GB387_22430, GB387_24570, GB396_24800, SOURCE 14 GB396_25405, GB407_23420, GB407_24705, GB492_23470, GB492_24085, SOURCE 15 GB502_23000, GB574_23445, GB574_24220, GB577_23875, GB577_24545, SOURCE 16 GBS28_23930, GBS32_23475, GBS32_24220, GBW29_23760, GBW29_24500, SOURCE 17 GBX88_23450, GBX88_24260, GBX94_22210, GBX94_24300, GBY07_22650, SOURCE 18 GBY14_22545, GBY14_24165, GBY50_23665, GBY50_24595, GBZ99_23255, SOURCE 19 GBZ99_24525, GDM15_22805, GDM15_25520, GDM77_24145, GDM77_25870, SOURCE 20 MB64_25285, MB64_25625; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 22 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS YDJB-LIKE PROTEIN, NICOTINAMIDASE, ASPARTOKINASE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.KANG,H.H.PARK,J.H.KIM REVDAT 1 22-OCT-25 9VP8 0 JRNL AUTH J.H.KIM,H.H.PARK,Y.J.KANG JRNL TITL CRYSTAL STRUCTURE OF YDJB FROM SALMONELLA ENTERICA SUBSP. JRNL TITL 2 ENTERICA SEROVAR TYPHI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10720 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 535 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 29.6400 - 3.0500 1.00 2690 141 0.1844 0.2093 REMARK 3 2 3.0500 - 2.4200 1.00 2536 134 0.2105 0.1935 REMARK 3 3 2.4200 - 2.1100 1.00 2502 130 0.1918 0.2516 REMARK 3 4 2.1100 - 1.9200 1.00 2457 130 0.1744 0.2004 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 991 REMARK 3 ANGLE : 0.764 1339 REMARK 3 CHIRALITY : 0.054 161 REMARK 3 PLANARITY : 0.005 172 REMARK 3 DIHEDRAL : 5.248 132 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 9VP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 125 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10725 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 29.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 25.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 8000 0.1M MES PH 6.0 0.2M REMARK 280 CA(OAC)2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 70.30000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.44000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.45000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.44000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.44000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.15000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.44000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.44000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.45000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.44000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.44000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.15000 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 70.30000 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: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 0.00000 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 A 312 LIES ON A SPECIAL POSITION. 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 O HOH A 295 O HOH A 304 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 A 257 O HOH A 288 7555 2.14 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 ASN A 115 64.78 -158.91 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9VP8 A 2 129 UNP A0A3T5P7Q7_SALET DBREF2 9VP8 A A0A3T5P7Q7 1 128 SEQADV 9VP8 MET A 1 UNP A0A3T5P7Q INITIATING METHIONINE SEQRES 1 A 129 MET MET PHE ASP VAL HIS VAL VAL LEU ASP ASN GLN ILE SEQRES 2 A 129 GLY GLN LEU ALA LEU LEU GLY LYS THR LEU GLY ASN LYS SEQRES 3 A 129 GLY ILE GLY LEU GLU GLY GLY GLY ILE PHE THR VAL GLY SEQRES 4 A 129 ASP GLU CYS HIS ALA HIS PHE LEU VAL GLU GLN GLY LYS SEQRES 5 A 129 GLU ALA LYS ILE ALA LEU GLU GLN ALA GLY LEU LEU VAL SEQRES 6 A 129 LEU ALA ILE ARG THR PRO LEU ILE ARG LYS LEU LYS GLN SEQRES 7 A 129 GLU LYS PRO GLY GLU LEU GLY GLU ILE ALA ARG VAL LEU SEQRES 8 A 129 ALA GLU ASN ASN ILE ASN ILE LEU VAL GLN TYR SER ASP SEQRES 9 A 129 HIS ALA ASN GLN LEU ILE LEU ILE THR ASP ASN ASP SER SEQRES 10 A 129 MET ALA ALA SER VAL THR LEU PRO TRP ALA ILE LYS FORMUL 2 HOH *112(H2 O) HELIX 1 AA1 GLY A 14 LYS A 26 1 13 HELIX 2 AA2 GLN A 50 ALA A 61 1 12 HELIX 3 AA3 GLY A 82 ASN A 94 1 13 HELIX 4 AA4 ASN A 115 THR A 123 1 9 HELIX 5 AA5 LEU A 124 ALA A 127 5 4 SHEET 1 AA1 4 GLY A 33 VAL A 38 0 SHEET 2 AA1 4 GLU A 41 VAL A 48 -1 O GLU A 41 N VAL A 38 SHEET 3 AA1 4 PHE A 3 ASP A 10 -1 N LEU A 9 O CYS A 42 SHEET 4 AA1 4 LEU A 64 ARG A 69 -1 O ARG A 69 N ASP A 4 SHEET 1 AA2 3 LEU A 72 ARG A 74 0 SHEET 2 AA2 3 LEU A 109 THR A 113 -1 O LEU A 109 N ARG A 74 SHEET 3 AA2 3 ILE A 98 SER A 103 -1 N TYR A 102 O ILE A 110 CRYST1 42.880 42.880 140.600 90.00 90.00 90.00 P 43 21 2 8 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 0.023321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007112 0.00000 MASTER 269 0 0 5 7 0 0 6 1091 1 0 10 END