HEADER TRANSCRIPTION 09-APR-24 8Z0C 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, B; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATOR,TETR FAMILY; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOCOCCACEAE; SOURCE 3 ORGANISM_TAXID: 403; SOURCE 4 GENE: ABCAM1_2317, ABUW_1678, ACX61_07530, B9X95_03330, DOL94_11245, SOURCE 5 EA686_06095, F2P40_10030, FJV09_06005, GNY86_03815, HB367_07475; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION FACTORS, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.B.YANG,N.WANG REVDAT 1 16-APR-25 8Z0C 0 JRNL AUTH B.B.YANG,N.WANG JRNL TITL CRYSTAL STRUCTURE OF A TETR FAMILY REGULATOR AMVR FROM JRNL TITL 2 ACINETOBACTER BAUMANNII WITH SPERMIDINE BOUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13420 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 29.9200 - 4.3569 1.00 2681 129 0.1900 0.2722 REMARK 3 2 4.3569 - 3.4599 1.00 2566 125 0.2213 0.2991 REMARK 3 3 3.4599 - 3.0230 1.00 2515 141 0.2698 0.3962 REMARK 3 4 3.0230 - 2.7468 1.00 2514 123 0.2847 0.3854 REMARK 3 5 2.7468 - 2.5500 1.00 2499 127 0.3178 0.3907 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.990 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 : 0.008 3070 REMARK 3 ANGLE : 0.962 4128 REMARK 3 CHIRALITY : 0.049 462 REMARK 3 PLANARITY : 0.004 534 REMARK 3 DIHEDRAL : 4.080 1864 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 8Z0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.979 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 40.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M SODIUM POTASSIUM PHOSPHATE PH REMARK 280 8.5 0.1 M BIS TRIS PROPANE PH 8.5 20 % W/V PEG 3350 10 % V/V REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.44500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.44500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.76000 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: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 46 NE2 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 NE2 GLN A 124 O GLN B 172 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 THR A 40 -155.34 -124.32 REMARK 500 ASN A 145 62.18 -103.52 REMARK 500 MET B 29 68.19 -100.38 REMARK 500 ALA B 89 24.13 -78.02 REMARK 500 ASN B 91 74.81 58.86 REMARK 500 ASN B 145 58.33 -114.37 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8Z0C A 7 192 UNP A0A0D5YGI2_ACIBA DBREF2 8Z0C A A0A0D5YGI2 7 192 DBREF1 8Z0C B 7 192 UNP A0A0D5YGI2_ACIBA DBREF2 8Z0C B A0A0D5YGI2 7 192 SEQRES 1 A 186 ASP GLN ARG ARG GLU MET ILE LEU GLN ALA ALA MET GLN SEQRES 2 A 186 ILE ALA LEU ALA GLU GLY PHE THR ALA MET THR VAL ARG SEQRES 3 A 186 ARG ILE ALA THR GLU ALA GLN THR SER THR GLY GLN VAL SEQRES 4 A 186 HIS HIS HIS PHE SER SER ALA SER HIS LEU LYS ALA GLU SEQRES 5 A 186 ALA PHE LEU LYS LEU MET GLU GLN LEU ASP GLU ILE GLU SEQRES 6 A 186 GLN THR LEU GLN THR THR SER GLN PHE GLN ARG LEU PHE SEQRES 7 A 186 ILE LEU LEU GLY ALA GLU ASN ILE ASP ARG LEU GLN PRO SEQRES 8 A 186 TYR LEU ARG LEU TRP ASN GLU ALA GLU LEU LEU ILE GLU SEQRES 9 A 186 GLN ASP ILE GLU ILE GLN LYS ALA TYR ASN LEU ALA MET SEQRES 10 A 186 GLN SER TRP HIS GLN ALA ILE VAL GLN SER ILE GLU CYS SEQRES 11 A 186 GLY GLN LYS GLU GLY GLU PHE LYS ASN ARG SER ASN SER SEQRES 12 A 186 THR ASP ILE ALA TRP ARG LEU ILE ALA PHE VAL CYS GLY SEQRES 13 A 186 LEU GLU GLY ILE TYR LYS LEU GLY LEU GLN GLY LEU ALA SEQRES 14 A 186 GLU GLU ASP PHE LYS ARG HIS THR GLU ALA ILE ILE ARG SEQRES 15 A 186 LEU GLU LEU LEU SEQRES 1 B 186 ASP GLN ARG ARG GLU MET ILE LEU GLN ALA ALA MET GLN SEQRES 2 B 186 ILE ALA LEU ALA GLU GLY PHE THR ALA MET THR VAL ARG SEQRES 3 B 186 ARG ILE ALA THR GLU ALA GLN THR SER THR GLY GLN VAL SEQRES 4 B 186 HIS HIS HIS PHE SER SER ALA SER HIS LEU LYS ALA GLU SEQRES 5 B 186 ALA PHE LEU LYS LEU MET GLU GLN LEU ASP GLU ILE GLU SEQRES 6 B 186 GLN THR LEU GLN THR THR SER GLN PHE GLN ARG LEU PHE SEQRES 7 B 186 ILE LEU LEU GLY ALA GLU ASN ILE ASP ARG LEU GLN PRO SEQRES 8 B 186 TYR LEU ARG LEU TRP ASN GLU ALA GLU LEU LEU ILE GLU SEQRES 9 B 186 GLN ASP ILE GLU ILE GLN LYS ALA TYR ASN LEU ALA MET SEQRES 10 B 186 GLN SER TRP HIS GLN ALA ILE VAL GLN SER ILE GLU CYS SEQRES 11 B 186 GLY GLN LYS GLU GLY GLU PHE LYS ASN ARG SER ASN SER SEQRES 12 B 186 THR ASP ILE ALA TRP ARG LEU ILE ALA PHE VAL CYS GLY SEQRES 13 B 186 LEU GLU GLY ILE TYR LYS LEU GLY LEU GLN GLY LEU ALA SEQRES 14 B 186 GLU GLU ASP PHE LYS ARG HIS THR GLU ALA ILE ILE ARG SEQRES 15 B 186 LEU GLU LEU LEU HET SPD A 201 10 HET SPD B 201 10 HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 3 SPD 2(C7 H19 N3) FORMUL 5 HOH *7(H2 O) HELIX 1 AA1 GLN A 8 GLY A 25 1 18 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 GLN A 72 1 22 HELIX 5 AA5 SER A 78 LEU A 87 1 10 HELIX 6 AA6 ILE A 92 ARG A 94 5 3 HELIX 7 AA7 LEU A 95 ILE A 109 1 15 HELIX 8 AA8 ASP A 112 LYS A 139 1 28 HELIX 9 AA9 ASN A 148 LYS A 168 1 21 HELIX 10 AB1 ALA A 175 GLU A 177 5 3 HELIX 11 AB2 ASP A 178 LEU A 192 1 15 HELIX 12 AB3 GLN B 8 GLY B 25 1 18 HELIX 13 AB4 PHE B 26 MET B 29 5 4 HELIX 14 AB5 THR B 30 ALA B 38 1 9 HELIX 15 AB6 SER B 41 PHE B 49 1 9 HELIX 16 AB7 SER B 51 GLN B 72 1 22 HELIX 17 AB8 SER B 78 LEU B 87 1 10 HELIX 18 AB9 LEU B 95 LEU B 108 1 14 HELIX 19 AC1 ASP B 112 GLU B 140 1 29 HELIX 20 AC2 ASN B 148 LEU B 169 1 22 HELIX 21 AC3 ALA B 175 GLU B 177 5 3 HELIX 22 AC4 ASP B 178 LEU B 191 1 14 CRYST1 59.840 65.520 100.890 90.00 90.00 90.00 P 21 21 21 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 0.016711 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009912 0.00000 CONECT 3009 3010 CONECT 3010 3009 3011 CONECT 3011 3010 3012 CONECT 3012 3011 3013 CONECT 3013 3012 3014 CONECT 3014 3013 3015 CONECT 3015 3014 3016 CONECT 3016 3015 3017 CONECT 3017 3016 3018 CONECT 3018 3017 CONECT 3019 3020 CONECT 3020 3019 3021 CONECT 3021 3020 3022 CONECT 3022 3021 3023 CONECT 3023 3022 3024 CONECT 3024 3023 3025 CONECT 3025 3024 3026 CONECT 3026 3025 3027 CONECT 3027 3026 3028 CONECT 3028 3027 MASTER 238 0 2 22 0 0 0 6 3033 2 20 30 END