HEADER HYDROLASE 01-APR-14 4Q0F TITLE CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA FTSH PERIPLASMIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: PERIPLASMIC DOMAIN, UNP RESIDUES 34-101; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: MSB8; SOURCE 5 GENE: FTSH, TM_0580; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATP-DEPENDENT PROTEOLYSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.AN,H.SHARIF,F.N.BARRERA,A.KARABADZHAK,G.B.KANG,K.J.PARK, AUTHOR 2 S.SAKKIAH,K.W.LEE,S.LEE,D.M.ENGELMAN,J.WANG,S.H.EOM REVDAT 1 01-APR-15 4Q0F 0 JRNL AUTH J.Y.AN,H.SHARIF,F.N.BARRERA,A.KARABADZHAK,G.B.KANG,K.J.PARK, JRNL AUTH 2 S.SAKKIAH,K.W.LEE,S.LEE,D.M.ENGELMAN,J.WANG,S.H.EOM JRNL TITL STRUCTURES OF PERIPLASMIC AND TRANSMEMBRANE DOMAINS OF FTSH JRNL TITL 2 SUGGEST A REVERSE TRANSLOCON MECHANISM FOR PROTEIN JRNL TITL 3 EXTRACTION FROM MEMBRANE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 756 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 36.3098 - 3.3295 0.99 3041 126 0.1902 0.2362 REMARK 3 2 3.3295 - 2.6430 1.00 2885 161 0.2138 0.2453 REMARK 3 3 2.6430 - 2.3089 1.00 2878 148 0.2158 0.2521 REMARK 3 4 2.3089 - 2.0979 0.99 2784 187 0.2394 0.2887 REMARK 3 5 2.0979 - 1.9475 0.97 2737 134 0.2334 0.2846 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.300 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 : 0.003 1617 REMARK 3 ANGLE : 0.639 2182 REMARK 3 CHIRALITY : 0.045 256 REMARK 3 PLANARITY : 0.002 276 REMARK 3 DIHEDRAL : 12.621 609 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 4Q0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-APR-14. REMARK 100 THE RCSB ID CODE IS RCSB085447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.97924, 0.97901, 0.97134, REMARK 200 0.98696 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.948 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (W/V) PEG 2000, 0.1M MES-NAOH (PH REMARK 280 6.0) , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 21.01600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.06250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.01600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.06250 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 84.06400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 132.25000 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 B 239 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 241 LIES ON A SPECIAL POSITION. 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 GLY A 30 REMARK 465 ALA A 31 REMARK 465 MSE A 32 REMARK 465 GLY A 33 REMARK 465 GLY B 30 REMARK 465 ALA B 31 REMARK 465 MSE B 32 REMARK 465 GLY B 33 REMARK 465 ARG B 101 REMARK 465 GLY C 30 REMARK 465 ALA C 31 REMARK 465 MSE C 32 REMARK 465 GLY C 33 REMARK 465 SER C 34 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 SER C 50 OG 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 ARG A 49 41.18 -100.30 REMARK 500 ALA A 77 83.47 -153.32 REMARK 500 ASN A 82 69.55 -116.44 REMARK 500 ALA B 77 77.56 -154.71 REMARK 500 SER C 50 100.07 -57.85 REMARK 500 ALA C 77 84.03 -156.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M8A RELATED DB: PDB REMARK 900 THE SAME PROTEIN DBREF 4Q0F A 34 101 UNP Q9WZ49 FTSH_THEMA 34 101 DBREF 4Q0F B 34 101 UNP Q9WZ49 FTSH_THEMA 34 101 DBREF 4Q0F C 34 101 UNP Q9WZ49 FTSH_THEMA 34 101 SEQADV 4Q0F GLY A 30 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F ALA A 31 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F MSE A 32 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F GLY A 33 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F GLY B 30 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F ALA B 31 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F MSE B 32 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F GLY B 33 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F GLY C 30 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F ALA C 31 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F MSE C 32 UNP Q9WZ49 EXPRESSION TAG SEQADV 4Q0F GLY C 33 UNP Q9WZ49 EXPRESSION TAG SEQRES 1 A 72 GLY ALA MSE GLY SER LYS LEU SER TYR THR SER PHE VAL SEQRES 2 A 72 GLN MSE VAL GLU ASP GLU ARG SER VAL VAL SER GLU VAL SEQRES 3 A 72 VAL ILE ARG ASP ASP GLY VAL LEU ARG VAL TYR THR LYS SEQRES 4 A 72 ASP GLY ARG VAL TYR GLU VAL ASP ALA PRO TRP ALA VAL SEQRES 5 A 72 ASN ASP SER GLN LEU ILE GLU LYS LEU VAL SER LYS GLY SEQRES 6 A 72 ILE LYS VAL SER GLY GLU ARG SEQRES 1 B 72 GLY ALA MSE GLY SER LYS LEU SER TYR THR SER PHE VAL SEQRES 2 B 72 GLN MSE VAL GLU ASP GLU ARG SER VAL VAL SER GLU VAL SEQRES 3 B 72 VAL ILE ARG ASP ASP GLY VAL LEU ARG VAL TYR THR LYS SEQRES 4 B 72 ASP GLY ARG VAL TYR GLU VAL ASP ALA PRO TRP ALA VAL SEQRES 5 B 72 ASN ASP SER GLN LEU ILE GLU LYS LEU VAL SER LYS GLY SEQRES 6 B 72 ILE LYS VAL SER GLY GLU ARG SEQRES 1 C 72 GLY ALA MSE GLY SER LYS LEU SER TYR THR SER PHE VAL SEQRES 2 C 72 GLN MSE VAL GLU ASP GLU ARG SER VAL VAL SER GLU VAL SEQRES 3 C 72 VAL ILE ARG ASP ASP GLY VAL LEU ARG VAL TYR THR LYS SEQRES 4 C 72 ASP GLY ARG VAL TYR GLU VAL ASP ALA PRO TRP ALA VAL SEQRES 5 C 72 ASN ASP SER GLN LEU ILE GLU LYS LEU VAL SER LYS GLY SEQRES 6 C 72 ILE LYS VAL SER GLY GLU ARG MODRES 4Q0F MSE A 44 MET SELENOMETHIONINE MODRES 4Q0F MSE B 44 MET SELENOMETHIONINE MODRES 4Q0F MSE C 44 MET SELENOMETHIONINE HET MSE A 44 8 HET MSE B 44 8 HET MSE C 44 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 4 HOH *87(H2 O) HELIX 1 1 SER A 37 ASP A 47 1 11 HELIX 2 2 TRP A 79 ASN A 82 5 4 HELIX 3 3 ASP A 83 LYS A 93 1 11 HELIX 4 4 SER B 37 ASP B 47 1 11 HELIX 5 5 PRO B 78 VAL B 81 5 4 HELIX 6 6 ASP B 83 LYS B 93 1 11 HELIX 7 7 SER C 37 ASP C 47 1 11 HELIX 8 8 PRO C 78 ASN C 82 5 5 HELIX 9 9 ASP C 83 LYS C 93 1 11 SHEET 1 A 4 VAL A 72 ASP A 76 0 SHEET 2 A 4 VAL A 62 THR A 67 -1 N LEU A 63 O VAL A 75 SHEET 3 A 4 VAL A 52 ARG A 58 -1 N GLU A 54 O TYR A 66 SHEET 4 A 4 LYS A 96 GLU A 100 1 O SER A 98 N ILE A 57 SHEET 1 B 4 VAL B 72 ASP B 76 0 SHEET 2 B 4 VAL B 62 THR B 67 -1 N LEU B 63 O VAL B 75 SHEET 3 B 4 VAL B 52 ARG B 58 -1 N GLU B 54 O TYR B 66 SHEET 4 B 4 LYS B 96 GLU B 100 1 O LYS B 96 N VAL B 55 SHEET 1 C 4 VAL C 72 ASP C 76 0 SHEET 2 C 4 VAL C 62 THR C 67 -1 N VAL C 65 O TYR C 73 SHEET 3 C 4 VAL C 52 ARG C 58 -1 N GLU C 54 O TYR C 66 SHEET 4 C 4 LYS C 96 GLU C 100 1 O LYS C 96 N VAL C 55 LINK C GLN A 43 N MSE A 44 1555 1555 1.33 LINK C MSE A 44 N VAL A 45 1555 1555 1.33 LINK C GLN B 43 N MSE B 44 1555 1555 1.33 LINK C MSE B 44 N VAL B 45 1555 1555 1.33 LINK C GLN C 43 N MSE C 44 1555 1555 1.33 LINK C MSE C 44 N VAL C 45 1555 1555 1.33 CRYST1 42.032 66.125 72.033 90.00 90.00 90.00 P 21 21 2 12 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 0.023791 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013883 0.00000