HEADER HYDROLASE 29-SEP-18 6IHG TITLE N TERMINAL DOMAIN OF MYCOBACTERIUM AVIUM COMPLEX LON PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LON PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: ATP-DEPENDENT PROTEASE LA; COMPND 6 EC: 3.4.21.53; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM [TUBERCULOSIS] TKK-01-0051; SOURCE 3 ORGANISM_TAXID: 1324261; SOURCE 4 GENE: LON, K875_02975; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS LON N-DOMAIN, HYDROLASE, ATP DEPENDENT EXPDTA X-RAY DIFFRACTION AUTHOR X.Y.CHEN,S.J.ZHANG,F.K.BI,C.Y.GUO,H.W.YAO,D.H.LIN REVDAT 3 22-NOV-23 6IHG 1 REMARK REVDAT 2 04-SEP-19 6IHG 1 JRNL REVDAT 1 07-AUG-19 6IHG 0 JRNL AUTH X.CHEN,S.ZHANG,F.BI,C.GUO,L.FENG,H.WANG,H.YAO,D.LIN JRNL TITL CRYSTAL STRUCTURE OF THE N DOMAIN OF LON PROTEASE FROM JRNL TITL 2 MYCOBACTERIUM AVIUM COMPLEX. JRNL REF PROTEIN SCI. V. 28 1720 2019 JRNL REFN ESSN 1469-896X JRNL PMID 31306520 JRNL DOI 10.1002/PRO.3687 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15RC2_3428: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 8942 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) : 0.227 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 24.8239 - 3.4555 1.00 3154 178 0.1863 0.2133 REMARK 3 2 3.4555 - 2.7439 1.00 3040 163 0.2609 0.3330 REMARK 3 3 2.7439 - 2.3974 0.76 2273 134 0.3292 0.3778 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.260 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 : 0.009 1430 REMARK 3 ANGLE : 1.091 1949 REMARK 3 CHIRALITY : 0.056 236 REMARK 3 PLANARITY : 0.005 251 REMARK 3 DIHEDRAL : 3.982 870 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 5:190) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4615 26.2422 13.2043 REMARK 3 T TENSOR REMARK 3 T11: 0.1938 T22: 0.2072 REMARK 3 T33: 0.2102 T12: 0.0243 REMARK 3 T13: -0.0056 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 1.2707 L22: 1.3257 REMARK 3 L33: 6.2317 L12: -0.3525 REMARK 3 L13: -0.1861 L23: 0.0413 REMARK 3 S TENSOR REMARK 3 S11: 0.1389 S12: -0.0592 S13: -0.1422 REMARK 3 S21: 0.0792 S22: 0.0229 S23: -0.0246 REMARK 3 S31: -0.0939 S32: -0.3031 S33: -0.0861 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 6IHG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-18 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.397 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 (%) : 91.8 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 3.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : 0.63000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6IHF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE,SODIUM ACETATE REMARK 280 TRIHYDRATE, LIQUID DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.42533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.85067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.85067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.42533 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 191 REMARK 465 GLU A 192 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 ASP A 54 20.82 -144.41 REMARK 500 ALA A 97 40.92 -107.67 REMARK 500 THR A 154 -36.46 -34.74 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6IHG A 1 192 UNP A0A051TYQ1_9MYCO DBREF2 6IHG A A0A051TYQ1 1 192 SEQADV 6IHG GLY A -2 UNP A0A051TYQ EXPRESSION TAG SEQADV 6IHG SER A -1 UNP A0A051TYQ EXPRESSION TAG SEQADV 6IHG HIS A 0 UNP A0A051TYQ EXPRESSION TAG SEQRES 1 A 195 GLY SER HIS MET ALA GLU ALA LYS SER VAL PRO VAL LEU SEQRES 2 A 195 PHE VAL THR ASP THR ILE VAL LEU PRO GLY MET VAL VAL SEQRES 3 A 195 PRO ILE ALA LEU ASP ASP THR ALA ARG ALA ALA ILE ASP SEQRES 4 A 195 ALA ALA GLN ALA SER GLU SER GLY GLN LEU LEU ILE ALA SEQRES 5 A 195 PRO ARG LEU GLU ASP ARG TYR PRO SER HIS GLY VAL ILE SEQRES 6 A 195 ALA LYS ILE LEU GLN VAL GLY ARG ILE ALA GLY GLY GLY SEQRES 7 A 195 THR ALA ALA VAL VAL ARG GLY GLU ARG ARG ALA GLN ILE SEQRES 8 A 195 GLY ALA GLY ALA SER GLY PRO GLY ALA ALA LEU TRP VAL SEQRES 9 A 195 GLU VAL THR GLU VAL PRO GLU ALA GLU ALA THR ASP GLU SEQRES 10 A 195 ILE LYS ALA LEU THR ALA GLU TYR LYS LYS LEU LEU LEU SEQRES 11 A 195 ALA MET LEU GLN ARG ARG GLU ALA TRP GLU ILE ILE ASP SEQRES 12 A 195 TYR VAL ASN ARG LEU THR ASP PRO SER ALA LEU ALA ASP SEQRES 13 A 195 THR SER GLY TYR ALA SER TYR LEU THR ASN ALA GLN LYS SEQRES 14 A 195 ARG GLN LEU LEU GLU THR VAL ASP VAL THR GLU ARG LEU SEQRES 15 A 195 ARG VAL LEU ILE ASP TRP THR SER ASP HIS LEU ALA GLU FORMUL 2 HOH *28(H2 O) HELIX 1 AA1 ASP A 28 SER A 41 1 14 HELIX 2 AA2 THR A 112 GLU A 134 1 23 HELIX 3 AA3 ALA A 135 LEU A 145 1 11 HELIX 4 AA4 ASP A 147 THR A 154 1 8 HELIX 5 AA5 SER A 155 ALA A 158 5 4 HELIX 6 AA6 THR A 162 GLU A 171 1 10 HELIX 7 AA7 ASP A 174 SER A 187 1 14 SHEET 1 AA1 7 VAL A 22 ALA A 26 0 SHEET 2 AA1 7 THR A 76 SER A 93 -1 O VAL A 80 N VAL A 23 SHEET 3 AA1 7 LEU A 99 GLU A 105 -1 O GLU A 102 N GLY A 89 SHEET 4 AA1 7 SER A 6 VAL A 12 -1 N VAL A 9 O LEU A 99 SHEET 5 AA1 7 GLN A 45 PRO A 50 1 O LEU A 47 N PRO A 8 SHEET 6 AA1 7 HIS A 59 ARG A 70 -1 O VAL A 61 N ILE A 48 SHEET 7 AA1 7 THR A 76 SER A 93 -1 O VAL A 79 N GLN A 67 CRYST1 58.631 58.631 118.276 90.00 90.00 120.00 P 31 2 1 6 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 0.017056 0.009847 0.000000 0.00000 SCALE2 0.000000 0.019694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008455 0.00000