HEADER TRANSCRIPTION 09-OCT-23 8WP7 TITLE CRYSTAL STRUCTURE OF A TETR FAMILY REGULATOR AMVR FROM ACINETOBACTER TITLE 2 BAUMANNII WITH SPERMIDINE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: ABCAM1_2317; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TETR FAMILY REGULATOR, EFFECTOR-BINDING DOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MA,H.H.GE,N.WANG REVDAT 1 16-APR-25 8WP7 0 JRNL AUTH J.M.MA,H.H.GE JRNL TITL CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII LYSR FAMILY JRNL TITL 2 REGULATOR ACER EFFECTOR BINDING DOMAIN (APO) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 878 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 35.1600 - 3.4600 1.00 3083 148 0.1705 0.1813 REMARK 3 2 3.4600 - 2.7500 1.00 2935 151 0.2033 0.2573 REMARK 3 3 2.7500 - 2.4000 1.00 2880 136 0.2080 0.2482 REMARK 3 4 2.4000 - 2.1800 1.00 2892 165 0.1909 0.2338 REMARK 3 5 2.1800 - 2.0300 1.00 2871 142 0.2101 0.2480 REMARK 3 6 2.0300 - 1.9100 0.99 2850 136 0.2487 0.2981 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.67 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 : 0.003 1535 REMARK 3 ANGLE : 0.564 2064 REMARK 3 CHIRALITY : 0.040 231 REMARK 3 PLANARITY : 0.003 267 REMARK 3 DIHEDRAL : 5.410 207 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 18.8677 27.2457 11.5422 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.2190 REMARK 3 T33: 0.2022 T12: -0.0153 REMARK 3 T13: -0.0080 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 0.4021 L22: 0.7840 REMARK 3 L33: 0.6400 L12: 0.5067 REMARK 3 L13: -0.4993 L23: -0.5654 REMARK 3 S TENSOR REMARK 3 S11: -0.0250 S12: 0.0807 S13: 0.0205 REMARK 3 S21: -0.0397 S22: 0.1197 S23: 0.0999 REMARK 3 S31: 0.0142 S32: -0.2298 S33: -0.0001 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 8WP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300039559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18423 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 47.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 (%): 53.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 10% V/V ETHYLENE REMARK 280 GLYCOL, 20% W/V PEG 3350, EVAPORATION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 -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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 32.13400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.15900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.13400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.15900 REMARK 290 SMTRY3 4 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: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 64.26800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 70.31800 REMARK 350 BIOMT3 2 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 ALA A 2 REMARK 465 TYR A 3 REMARK 465 LEU A 4 REMARK 465 ASN A 5 REMARK 465 ARG A 6 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 91 76.29 54.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 440 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 441 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 442 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 443 DISTANCE = 6.37 ANGSTROMS DBREF1 8WP7 A 1 192 UNP A0A0D5YGI2_ACIBA DBREF2 8WP7 A A0A0D5YGI2 1 192 SEQRES 1 A 192 MET ALA TYR LEU ASN ARG ASP GLN ARG ARG GLU MET ILE SEQRES 2 A 192 LEU GLN ALA ALA MET GLN ILE ALA LEU ALA GLU GLY PHE SEQRES 3 A 192 THR ALA MET THR VAL ARG ARG ILE ALA THR GLU ALA GLN SEQRES 4 A 192 THR SER THR GLY GLN VAL HIS HIS HIS PHE SER SER ALA SEQRES 5 A 192 SER HIS LEU LYS ALA GLU ALA PHE LEU LYS LEU MET GLU SEQRES 6 A 192 GLN LEU ASP GLU ILE GLU GLN THR LEU GLN THR THR SER SEQRES 7 A 192 GLN PHE GLN ARG LEU PHE ILE LEU LEU GLY ALA GLU ASN SEQRES 8 A 192 ILE ASP ARG LEU GLN PRO TYR LEU ARG LEU TRP ASN GLU SEQRES 9 A 192 ALA GLU LEU LEU ILE GLU GLN ASP ILE GLU ILE GLN LYS SEQRES 10 A 192 ALA TYR ASN LEU ALA MET GLN SER TRP HIS GLN ALA ILE SEQRES 11 A 192 VAL GLN SER ILE GLU CYS GLY GLN LYS GLU GLY GLU PHE SEQRES 12 A 192 LYS ASN ARG SER ASN SER THR ASP ILE ALA TRP ARG LEU SEQRES 13 A 192 ILE ALA PHE VAL CYS GLY LEU GLU GLY ILE TYR LYS LEU SEQRES 14 A 192 GLY LEU GLN GLY LEU ALA GLU GLU ASP PHE LYS ARG HIS SEQRES 15 A 192 THR GLU ALA ILE ILE ARG LEU GLU LEU LEU HET SPD A 201 10 HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 SPD C7 H19 N3 FORMUL 3 HOH *143(H2 O) HELIX 1 AA1 ASP A 7 GLY A 25 1 19 HELIX 2 AA2 THR A 30 GLN A 39 1 10 HELIX 3 AA3 SER A 41 PHE A 49 1 9 HELIX 4 AA4 SER A 51 LEU A 74 1 24 HELIX 5 AA5 SER A 78 LEU A 87 1 10 HELIX 6 AA6 LEU A 95 ILE A 109 1 15 HELIX 7 AA7 ASP A 112 GLU A 140 1 29 HELIX 8 AA8 ASN A 148 LYS A 168 1 21 HELIX 9 AA9 ALA A 175 GLU A 177 5 3 HELIX 10 AB1 ASP A 178 LEU A 192 1 15 CRYST1 64.268 70.318 50.370 90.00 90.00 90.00 P 21 21 2 4 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 0.015560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019853 0.00000 CONECT 1505 1506 CONECT 1506 1505 1507 CONECT 1507 1506 1508 CONECT 1508 1507 1509 CONECT 1509 1508 1510 CONECT 1510 1509 1511 CONECT 1511 1510 1512 CONECT 1512 1511 1513 CONECT 1513 1512 1514 CONECT 1514 1513 MASTER 262 0 1 10 0 0 0 6 1656 1 10 15 END