HEADER TRANSCRIPTION 11-JUL-24 9IPT 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 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 2 28-JAN-26 9IPT 1 JRNL REVDAT 1 16-JUL-25 9IPT 0 JRNL AUTH N.WANG,X.WANG,M.ZHOU,Q.LU,Y.XU,Y.WANG,H.WANG,B.YANG,S.HE, JRNL AUTH 2 L.XU,J.LI,H.GE,J.MA JRNL TITL STRUCTURAL BASIS FOR SPERMIDINE RECOGNITION AND MODULATION JRNL TITL 2 OF ACINETOBACTER BAUMANNII MULTIDRUG EFFLUX REGULATOR AMVR. JRNL REF MBIO V. 16 08125 2025 JRNL REFN ESSN 2150-7511 JRNL PMID 40162807 JRNL DOI 10.1128/MBIO.00081-25 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14245 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) : 0.229 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 673 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 29.9500 - 4.2700 1.00 2847 145 0.1917 0.2165 REMARK 3 2 4.2700 - 3.3900 1.00 2719 142 0.2160 0.2880 REMARK 3 3 3.3900 - 2.9600 0.99 2690 126 0.2763 0.3237 REMARK 3 4 2.9600 - 2.6900 1.00 2676 137 0.2872 0.3523 REMARK 3 5 2.6900 - 2.5000 0.99 2640 123 0.3507 0.3647 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.20 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 : 0.002 3045 REMARK 3 ANGLE : 0.457 4098 REMARK 3 CHIRALITY : 0.033 462 REMARK 3 PLANARITY : 0.003 529 REMARK 3 DIHEDRAL : 5.375 413 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): 15.1069 0.2647 14.6578 REMARK 3 T TENSOR REMARK 3 T11: 0.5039 T22: 0.6036 REMARK 3 T33: 0.3189 T12: -0.0058 REMARK 3 T13: 0.0048 T23: -0.0496 REMARK 3 L TENSOR REMARK 3 L11: 0.6699 L22: 1.5314 REMARK 3 L33: 3.1614 L12: 0.5573 REMARK 3 L13: -0.7095 L23: -1.6957 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: -0.0156 S13: 0.0282 REMARK 3 S21: 0.0303 S22: 0.0789 S23: 0.1283 REMARK 3 S31: 0.1251 S32: -0.0584 S33: -0.1006 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 9IPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049332. 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) : 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.43 REMARK 200 R MERGE (I) : 0.17310 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.38570 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 46.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 10% V/V ETHYLENE REMARK 280 GLYCOL, 20% W/V PEG 3350, VAPOR DIFFUSION, 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 30.00250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.51600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.51600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.00250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.75500 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 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 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 465 ASP A 7 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 TYR B 3 REMARK 465 LEU B 4 REMARK 465 ASN B 5 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 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 44 CG CD OE1 NE2 REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 ARG B 6 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 8 CG CD OE1 NE2 REMARK 470 GLN B 81 CG CD OE1 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 ALA A 23 -72.03 -111.93 REMARK 500 ASN A 145 61.31 -106.18 REMARK 500 MET B 29 48.75 -95.50 REMARK 500 THR B 77 -79.82 -102.55 REMARK 500 ASN B 91 82.94 59.24 REMARK 500 ASN B 145 49.94 -106.67 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9IPT A 1 192 UNP A0A0D5YGI2_ACIBA DBREF2 9IPT A A0A0D5YGI2 1 192 DBREF1 9IPT B 1 192 UNP A0A0D5YGI2_ACIBA DBREF2 9IPT B 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 SEQRES 1 B 192 MET ALA TYR LEU ASN ARG ASP GLN ARG ARG GLU MET ILE SEQRES 2 B 192 LEU GLN ALA ALA MET GLN ILE ALA LEU ALA GLU GLY PHE SEQRES 3 B 192 THR ALA MET THR VAL ARG ARG ILE ALA THR GLU ALA GLN SEQRES 4 B 192 THR SER THR GLY GLN VAL HIS HIS HIS PHE SER SER ALA SEQRES 5 B 192 SER HIS LEU LYS ALA GLU ALA PHE LEU LYS LEU MET GLU SEQRES 6 B 192 GLN LEU ASP GLU ILE GLU GLN THR LEU GLN THR THR SER SEQRES 7 B 192 GLN PHE GLN ARG LEU PHE ILE LEU LEU GLY ALA GLU ASN SEQRES 8 B 192 ILE ASP ARG LEU GLN PRO TYR LEU ARG LEU TRP ASN GLU SEQRES 9 B 192 ALA GLU LEU LEU ILE GLU GLN ASP ILE GLU ILE GLN LYS SEQRES 10 B 192 ALA TYR ASN LEU ALA MET GLN SER TRP HIS GLN ALA ILE SEQRES 11 B 192 VAL GLN SER ILE GLU CYS GLY GLN LYS GLU GLY GLU PHE SEQRES 12 B 192 LYS ASN ARG SER ASN SER THR ASP ILE ALA TRP ARG LEU SEQRES 13 B 192 ILE ALA PHE VAL CYS GLY LEU GLU GLY ILE TYR LYS LEU SEQRES 14 B 192 GLY LEU GLN GLY LEU ALA GLU GLU ASP PHE LYS ARG HIS SEQRES 15 B 192 THR GLU ALA ILE ILE ARG 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) HELIX 1 AA1 GLN A 8 GLU A 24 1 17 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 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 LEU A 169 1 22 HELIX 9 AA9 ALA A 175 GLU A 177 5 3 HELIX 10 AB1 ASP A 178 LEU A 192 1 15 HELIX 11 AB2 ASP B 7 GLU B 24 1 18 HELIX 12 AB3 THR B 30 ALA B 38 1 9 HELIX 13 AB4 SER B 41 PHE B 49 1 9 HELIX 14 AB5 SER B 51 THR B 73 1 23 HELIX 15 AB6 SER B 78 LEU B 87 1 10 HELIX 16 AB7 LEU B 95 LEU B 107 1 13 HELIX 17 AB8 ASP B 112 GLU B 140 1 29 HELIX 18 AB9 ASN B 148 LEU B 169 1 22 HELIX 19 AC1 ALA B 175 GLU B 177 5 3 HELIX 20 AC2 ASP B 178 LEU B 191 1 14 CRYST1 60.005 65.510 101.032 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 0.016665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009898 0.00000 CONECT 2984 2985 CONECT 2985 2984 2986 CONECT 2986 2985 2987 CONECT 2987 2986 2988 CONECT 2988 2987 2989 CONECT 2989 2988 2990 CONECT 2990 2989 2991 CONECT 2991 2990 2992 CONECT 2992 2991 2993 CONECT 2993 2992 CONECT 2994 2995 CONECT 2995 2994 2996 CONECT 2996 2995 2997 CONECT 2997 2996 2998 CONECT 2998 2997 2999 CONECT 2999 2998 3000 CONECT 3000 2999 3001 CONECT 3001 3000 3002 CONECT 3002 3001 3003 CONECT 3003 3002 MASTER 262 0 2 20 0 0 0 6 3001 2 20 30 END