HEADER MEMBRANE PROTEIN 27-OCT-23 8US4 TITLE C2221 CRYSTAL STRUCTURE OF TAMA (BARREL ONLY) FROM PSEUDOMONAS TITLE 2 AERUGINOSA AT 3.15 ANG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLOCATION AND ASSEMBLY MODULE SUBUNIT TAMA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATURE TAMA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 SOURCE 5 / 1C / PRS 101 / PAO1; SOURCE 6 GENE: PA2543; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS OMP85, PROTEIN TRANSLOCATION, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.MELLOUK,T.F.MORAES,C.CALMETTES REVDAT 1 26-JUN-24 8US4 0 JRNL AUTH A.MELLOUK,P.L.JAOUEN,L.J.RUEL,M.LE,C.MARTINI,T.F.MORAES, JRNL AUTH 2 M.EL BAKKOURI,P.LAGUE,E.BOISSELIER,C.CALMETTES JRNL TITL POTRA DOMAINS OF THE TAMA INSERTASE INTERACT WITH THE OUTER JRNL TITL 2 MEMBRANE AND MODULATE MEMBRANE PROPERTIES JRNL REF PROC.NATL.ACAD.SCI.USA 2024 JRNL REFN ESSN 1091-6490 JRNL DOI 10.1073/PNAS.2402543121 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 12152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.300 REMARK 3 FREE R VALUE : 0.350 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 88.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.08 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8US4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 ANG REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 3.3.20 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12152 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.988 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16800 REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : 0.58000 REMARK 200 FOR SHELL : 1.200 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 (%): 57.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 4K, 50 MM MGCL2, 70 MM HEPES REMARK 280 PH 7.2, 4% ISOPROPANOL, 10% GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 26.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.98750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.93800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.98750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.93800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.81000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.98750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.93800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.81000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.98750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.93800 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 GLU A 578 REMARK 465 LEU A 579 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 402 N - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 PRO A 407 C - N - CA ANGL. DEV. = -9.5 DEGREES 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 LEU A 324 -117.78 -93.91 REMARK 500 VAL A 344 -103.96 52.44 REMARK 500 ASP A 382 58.40 -108.21 REMARK 500 ASP A 383 -167.60 -160.75 REMARK 500 ALA A 444 -141.15 52.72 REMARK 500 ASP A 462 74.85 -156.10 REMARK 500 SER A 479 -84.68 -133.61 REMARK 500 ASP A 565 -137.48 50.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 403 LYS A 404 -149.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 8US4 A 272 579 UNP Q9I0U1 Q9I0U1_PSEAE 272 579 SEQRES 1 A 308 THR MET GLY VAL GLY LEU GLY PHE SER THR ASP VAL GLY SEQRES 2 A 308 ALA ARG ALA ARG PHE ASN TRP THR ARG HIS TRP VAL ASN SEQRES 3 A 308 ALA GLU GLY HIS SER LEU GLY PHE GLU SER GLU ILE SER SEQRES 4 A 308 ALA PRO ARG GLN ASN VAL GLY ALA TRP TYR GLU ILE PRO SEQRES 5 A 308 LEU ASP PRO PRO LEU THR ASP LYS LEU ARG PHE THR SER SEQRES 6 A 308 GLY TYR GLN PHE GLU ASP LEU VAL ASP THR GLU SER LYS SEQRES 7 A 308 LEU LEU THR LEU GLY GLY GLU TRP HIS SER LYS ARG PRO SEQRES 8 A 308 ASP GLY TRP GLN ARG VAL VAL SER LEU ASN TRP MET ARG SEQRES 9 A 308 GLU GLU TYR LYS LEU GLY ASP ASP SER GLY LEU SER SER SEQRES 10 A 308 PHE LEU MET PRO GLY ILE GLY TYR SER LEU LEU GLU THR SEQRES 11 A 308 ASP ASN LYS VAL ASP PRO SER HIS GLY TYR ARG LEU GLN SEQRES 12 A 308 PHE ASN VAL LYS GLY ALA LYS GLU GLY LEU LEU ALA ASP SEQRES 13 A 308 ALA ASP VAL LEU HIS VAL ASP ALA MET ALA LYS GLY LEU SEQRES 14 A 308 THR SER PHE ALA GLY GLY HIS ARG LEU LEU GLY ARG LEU SEQRES 15 A 308 GLN VAL GLY GLY ILE ALA THR ASN ASP TYR LYS SER ILE SEQRES 16 A 308 PRO PRO SER LEU ARG PHE PHE ALA GLY GLY ASP GLN SER SEQRES 17 A 308 VAL ARG GLY TYR ASP TYR ARG THR LEU SER PRO GLU ASN SEQRES 18 A 308 SER ASP GLY ASP LYS ILE GLY GLY ARG TYR MET ILE ALA SEQRES 19 A 308 GLY SER VAL GLU TYR GLN TYR PRO LEU ALA GLU ARG TRP SEQRES 20 A 308 ARG LEU ALA THR PHE VAL ASP GLN GLY ASN ALA PHE ASN SEQRES 21 A 308 SER LEU ASP PHE PRO SER ILE LYS THR GLY VAL GLY PHE SEQRES 22 A 308 GLY VAL ARG TRP VAL SER PRO VAL GLY PRO LEU ARG LEU SEQRES 23 A 308 ASP LEU ALA HIS ALA LEU ASP ASP ASP GLY GLY PHE ARG SEQRES 24 A 308 LEU HIS PHE SER MET GLY PRO GLU LEU HET PT A 601 1 HET PT A 602 1 HET PT A 603 1 HET PT A 604 1 HET PT A 605 1 HETNAM PT PLATINUM (II) ION FORMUL 2 PT 5(PT 2+) HELIX 1 AA1 ASP A 462 ILE A 466 5 5 HELIX 2 AA2 PRO A 467 ARG A 471 5 5 SHEET 1 AA116 MET A 273 GLY A 278 0 SHEET 2 AA116 ARG A 286 ARG A 293 -1 O ASN A 290 N GLY A 274 SHEET 3 AA116 SER A 302 SER A 310 -1 O ILE A 309 N ALA A 287 SHEET 4 AA116 ARG A 313 PRO A 323 -1 O GLU A 321 N SER A 302 SHEET 5 AA116 LYS A 331 LEU A 343 -1 O PHE A 340 N GLN A 314 SHEET 6 AA116 THR A 346 LYS A 360 -1 O THR A 346 N LEU A 343 SHEET 7 AA116 GLN A 366 LEU A 380 -1 O TRP A 373 N LEU A 353 SHEET 8 AA116 GLY A 385 THR A 401 -1 O GLY A 393 N SER A 370 SHEET 9 AA116 GLY A 410 ALA A 420 -1 O VAL A 417 N ILE A 394 SHEET 10 AA116 VAL A 430 PHE A 443 -1 O HIS A 432 N LYS A 418 SHEET 11 AA116 HIS A 447 THR A 460 -1 O GLY A 451 N GLY A 439 SHEET 12 AA116 TYR A 502 ALA A 515 -1 O GLU A 509 N LEU A 450 SHEET 13 AA116 TRP A 518 PHE A 530 -1 O GLN A 526 N GLY A 506 SHEET 14 AA116 LYS A 539 SER A 550 -1 O ARG A 547 N ARG A 519 SHEET 15 AA116 GLY A 553 ALA A 562 -1 O LEU A 555 N TRP A 548 SHEET 16 AA116 PHE A 569 SER A 574 -1 O SER A 574 N ARG A 556 CISPEP 1 ASP A 325 PRO A 326 0 -1.74 CRYST1 97.975 149.876 53.620 90.00 90.00 90.00 C 2 2 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 0.010207 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018650 0.00000