HEADER TRANSFERASE 18-AUG-12 4GO5 TITLE THE REGULATORY SUBUNIT OF ASPARTATE KINASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTOKINASE; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: REGULATORY SUBUNIT (UNP RESIDUES 250-421); COMPND 5 SYNONYM: ASPARTATE KINASE, ASK; COMPND 6 EC: 2.7.2.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: ASK, RV3709C, MT3812, MTV025.057C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.YANG,X.LI REVDAT 2 28-FEB-24 4GO5 1 SEQADV REVDAT 1 05-SEP-12 4GO5 0 JRNL AUTH Q.YANG,K.YU,L.YAN,Y.LI,C.CHEN,X.LI JRNL TITL STRUCTURAL VIEW OF THE REGULATORY SUBUNIT OF ASPARTATE JRNL TITL 2 KINASE FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF PROTEIN CELL V. 2 745 2011 JRNL REFN ISSN 1674-800X JRNL PMID 21976064 JRNL DOI 10.1007/S13238-011-1094-2 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 412 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 38.0842 - 3.7492 1.00 2797 114 0.1944 0.2289 REMARK 3 2 3.7492 - 2.9762 1.00 2758 136 0.2081 0.2565 REMARK 3 3 2.9762 - 2.6001 1.00 2724 162 0.2507 0.3035 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 45.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.590 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) : 3.04000 REMARK 3 B22 (A**2) : 3.04000 REMARK 3 B33 (A**2) : -6.08010 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1256 REMARK 3 ANGLE : 1.157 1703 REMARK 3 CHIRALITY : 0.073 208 REMARK 3 PLANARITY : 0.005 221 REMARK 3 DIHEDRAL : 16.108 448 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 4GO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM PHOSPHATE, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 32.39550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 32.39550 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.49050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.39550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.24525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.39550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.73575 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.39550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.39550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.49050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 32.39550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 102.73575 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 32.39550 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.24525 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: 3360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 X 212 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 MET X -19 REMARK 465 GLY X -18 REMARK 465 HIS X -14 REMARK 465 HIS X -13 REMARK 465 HIS X -12 REMARK 465 HIS X -11 REMARK 465 HIS X -10 REMARK 465 SER X -9 REMARK 465 SER X -8 REMARK 465 GLY X -7 REMARK 465 LEU X -6 REMARK 465 VAL X -5 REMARK 465 PRO X -4 REMARK 465 ARG X -3 REMARK 465 GLY X -2 REMARK 465 ASN X -1 REMARK 465 HIS X 0 REMARK 465 SER X 52 REMARK 465 LYS X 53 REMARK 465 VAL X 54 REMARK 465 GLU X 55 REMARK 465 GLY X 169 REMARK 465 THR X 170 REMARK 465 GLY X 171 REMARK 465 ARG X 172 REMARK 465 LEU X 173 REMARK 465 GLU X 174 REMARK 465 HIS X 175 REMARK 465 HIS X 176 REMARK 465 HIS X 177 REMARK 465 HIS X 178 REMARK 465 HIS X 179 REMARK 465 HIS X 180 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GO7 RELATED DB: PDB DBREF 4GO5 X 1 172 UNP P0A4Z8 AK_MYCTU 250 421 SEQADV 4GO5 MET X -19 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 GLY X -18 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 SER X -17 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 ILE X -16 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -15 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -14 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -13 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -12 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -11 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X -10 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 SER X -9 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 SER X -8 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 GLY X -7 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 LEU X -6 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 VAL X -5 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 PRO X -4 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 ARG X -3 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 GLY X -2 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 ASN X -1 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 0 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 LEU X 173 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 GLU X 174 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 175 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 176 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 177 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 178 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 179 UNP P0A4Z8 EXPRESSION TAG SEQADV 4GO5 HIS X 180 UNP P0A4Z8 EXPRESSION TAG SEQRES 1 X 200 MET GLY SER ILE HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 X 200 LEU VAL PRO ARG GLY ASN HIS MET GLU ASP PRO ILE LEU SEQRES 3 X 200 THR GLY VAL ALA HIS ASP ARG SER GLU ALA LYS VAL THR SEQRES 4 X 200 ILE VAL GLY LEU PRO ASP ILE PRO GLY TYR ALA ALA LYS SEQRES 5 X 200 VAL PHE ARG ALA VAL ALA ASP ALA ASP VAL ASN ILE ASP SEQRES 6 X 200 MET VAL LEU GLN ASN VAL SER LYS VAL GLU ASP GLY LYS SEQRES 7 X 200 THR ASP ILE THR PHE THR CYS SER ARG ASP VAL GLY PRO SEQRES 8 X 200 ALA ALA VAL GLU LYS LEU ASP SER LEU ARG ASN GLU ILE SEQRES 9 X 200 GLY PHE SER GLN LEU LEU TYR ASP ASP HIS ILE GLY LYS SEQRES 10 X 200 VAL SER LEU ILE GLY ALA GLY MET ARG SER HIS PRO GLY SEQRES 11 X 200 VAL THR ALA THR PHE CYS GLU ALA LEU ALA ALA VAL GLY SEQRES 12 X 200 VAL ASN ILE GLU LEU ILE SER THR SER GLU ILE ARG ILE SEQRES 13 X 200 SER VAL LEU CYS ARG ASP THR GLU LEU ASP LYS ALA VAL SEQRES 14 X 200 VAL ALA LEU HIS GLU ALA PHE GLY LEU GLY GLY ASP GLU SEQRES 15 X 200 GLU ALA THR VAL TYR ALA GLY THR GLY ARG LEU GLU HIS SEQRES 16 X 200 HIS HIS HIS HIS HIS FORMUL 2 HOH *20(H2 O) HELIX 1 1 GLY X 28 ALA X 40 1 13 HELIX 2 2 VAL X 69 LEU X 80 1 12 HELIX 3 3 GLY X 104 SER X 107 5 4 HELIX 4 4 HIS X 108 VAL X 122 1 15 HELIX 5 5 GLU X 144 PHE X 156 1 13 SHEET 1 A 6 ASP X 45 ASN X 50 0 SHEET 2 A 6 LYS X 58 SER X 66 -1 O ASP X 60 N ASN X 50 SHEET 3 A 6 ILE X 5 PRO X 24 -1 N LEU X 23 O THR X 59 SHEET 4 A 6 GLN X 88 ALA X 103 -1 O LEU X 90 N THR X 19 SHEET 5 A 6 ARG X 135 ARG X 141 -1 O CYS X 140 N GLY X 96 SHEET 6 A 6 LEU X 128 THR X 131 -1 N SER X 130 O SER X 137 SHEET 1 B 4 ASP X 45 ASN X 50 0 SHEET 2 B 4 LYS X 58 SER X 66 -1 O ASP X 60 N ASN X 50 SHEET 3 B 4 ILE X 5 PRO X 24 -1 N LEU X 23 O THR X 59 SHEET 4 B 4 THR X 165 VAL X 166 -1 O THR X 165 N LEU X 6 CISPEP 1 LEU X 158 GLY X 159 0 -0.87 CISPEP 2 GLY X 160 ASP X 161 0 1.65 CRYST1 64.791 64.791 136.981 90.00 90.00 90.00 I 41 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 0.015434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007300 0.00000