HEADER TRANSFERASE 29-DEC-09 3L83 OBSLTE 16-JUN-10 3L83 3M3P TITLE CRYSTAL STRUCTURE OF GLUTAMINE AMIDO TRANSFERASE FROM METHYLOBACILLUS TITLE 2 FLAGELLATUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE AMIDO TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOBACILLUS FLAGELLATUS; SOURCE 3 ORGANISM_TAXID: 265072; SOURCE 4 STRAIN: KT / ATCC 51484 / DSM 6875; SOURCE 5 GENE: MFLA_0438; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, NYSGRC, GLUTAMINE AMIDO TRANSFERASE, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, NYSGXRC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,R.TORO,M.J.SAUDER,S.K.BURLEY,S.C.ALMO,NEW AUTHOR 2 YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 2 16-JUN-10 3L83 1 OBSLTE REVDAT 1 12-JAN-10 3L83 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,R.TORO,M.J.SAUDER,S.K.BURLEY, JRNL AUTH 2 S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF GLUTAMINE AMIDO TRANSFERASE FROM JRNL TITL 2 METHYLOBACILLUS FLAGELLATUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 829569.990 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 34771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1750 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1997 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 118 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1859 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -1.67000 REMARK 3 B12 (A**2) : -1.77000 REMARK 3 B13 (A**2) : 0.32000 REMARK 3 B23 (A**2) : 0.69000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : -0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.88 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.340 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 50.07 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : &_1_PARAMETER_INFILE_4 REMARK 3 PARAMETER FILE 5 : &_1_PARAMETER_INFILE_5 REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3L83 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB056951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08100 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG3350, 0.2M SODIUM FORMATE, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 242 REMARK 465 GLU A 243 REMARK 465 GLY A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 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 GLU A 15 79.20 -106.05 REMARK 500 CYS A 89 -110.91 55.15 REMARK 500 TRP A 139 74.46 -168.48 REMARK 500 LEU A 169 -37.54 -138.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11175J RELATED DB: TARGETDB DBREF 3L83 A 4 242 UNP Q1H479 Q1H479_METFK 2 240 SEQADV 3L83 MET A 1 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 SER A 2 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 LEU A 3 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 GLU A 243 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 GLY A 244 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 245 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 246 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 247 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 248 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 249 UNP Q1H479 EXPRESSION TAG SEQADV 3L83 HIS A 250 UNP Q1H479 EXPRESSION TAG SEQRES 1 A 250 MET SER LEU LYS PRO VAL MET ILE ILE GLN PHE SER ALA SEQRES 2 A 250 SER GLU GLY PRO GLY HIS PHE GLY ASP PHE LEU ALA GLY SEQRES 3 A 250 GLU HIS ILE PRO PHE GLN VAL LEU ARG MET ASP ARG SER SEQRES 4 A 250 ASP PRO LEU PRO ALA GLU ILE ARG ASP CYS SER GLY LEU SEQRES 5 A 250 ALA MET MET GLY GLY PRO MET SER ALA ASN ASP ASP LEU SEQRES 6 A 250 PRO TRP MET PRO THR LEU LEU ALA LEU ILE ARG ASP ALA SEQRES 7 A 250 VAL ALA GLN ARG VAL PRO VAL ILE GLY HIS CYS LEU GLY SEQRES 8 A 250 GLY GLN LEU LEU ALA LYS ALA MET GLY GLY GLU VAL THR SEQRES 9 A 250 ASP SER PRO HIS ALA GLU ILE GLY TRP VAL ARG ALA TRP SEQRES 10 A 250 PRO GLN HIS VAL PRO GLN ALA LEU GLU TRP LEU GLY THR SEQRES 11 A 250 TRP ASP GLU LEU GLU LEU PHE GLU TRP HIS TYR GLN THR SEQRES 12 A 250 PHE SER ILE PRO PRO GLY ALA VAL HIS ILE LEU ARG SER SEQRES 13 A 250 GLU HIS CYS ALA ASN GLN ALA TYR VAL LEU ASP ASP LEU SEQRES 14 A 250 HIS ILE GLY PHE GLN CYS HIS ILE GLU MET GLN ALA HIS SEQRES 15 A 250 MET VAL ARG GLU TRP CYS SER ILE SER PRO GLU GLU LEU SEQRES 16 A 250 LYS GLY GLY ALA GLU ALA ASP PRO ALA GLN PRO MET VAL SEQRES 17 A 250 GLN SER ALA VAL GLU ILE LEU ARG ASP LEU ASP VAL ARG SEQRES 18 A 250 ILE ALA THR LEU ASN ARG TRP ALA GLU HIS VAL TYR ALA SEQRES 19 A 250 ARG TRP ILE LYS GLY LEU GLN ARG GLU GLY HIS HIS HIS SEQRES 20 A 250 HIS HIS HIS FORMUL 2 HOH *330(H2 O) HELIX 1 1 GLY A 18 GLU A 27 1 10 HELIX 2 2 ASP A 37 SER A 39 5 3 HELIX 3 3 GLU A 45 CYS A 49 5 5 HELIX 4 4 TRP A 67 GLN A 81 1 15 HELIX 5 5 CYS A 89 MET A 99 1 11 HELIX 6 6 VAL A 121 GLY A 129 1 9 HELIX 7 7 GLN A 180 SER A 191 1 12 HELIX 8 8 PRO A 192 LEU A 195 5 4 HELIX 9 9 SER A 210 ARG A 216 1 7 HELIX 10 10 ASP A 217 ILE A 237 1 21 HELIX 11 11 LYS A 238 LEU A 240 5 3 SHEET 1 A 9 PHE A 31 ARG A 35 0 SHEET 2 A 9 VAL A 6 GLN A 10 1 N GLN A 10 O LEU A 34 SHEET 3 A 9 GLY A 51 MET A 54 1 O ALA A 53 N ILE A 9 SHEET 4 A 9 VAL A 85 HIS A 88 1 O HIS A 88 N MET A 54 SHEET 5 A 9 HIS A 170 PHE A 173 1 O PHE A 173 N GLY A 87 SHEET 6 A 9 ALA A 163 LEU A 166 -1 N LEU A 166 O HIS A 170 SHEET 7 A 9 ALA A 150 SER A 156 -1 N VAL A 151 O VAL A 165 SHEET 8 A 9 VAL A 103 PRO A 118 -1 N TRP A 117 O ARG A 155 SHEET 9 A 9 LEU A 134 PHE A 144 -1 O GLU A 138 N GLY A 112 CRYST1 33.648 42.720 50.448 65.85 77.41 69.82 P 1 1 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 0.029719 -0.010922 -0.002853 0.00000 SCALE2 0.000000 0.024939 -0.009764 0.00000 SCALE3 0.000000 0.000000 0.021812 0.00000