HEADER TRANSCRIPTION 05-JUN-20 6ZAB TITLE STRUCTURE OF THE TRANSCRIPTIONAL REPRESSOR ATU1419 (VANR) FROM TITLE 2 AGROBACTERIUM FABRUM IN COMPLEX A PALINDROMIC DNA (P6422 SPACE GROUP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, GNTR FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM FABRUM (STRAIN C58 / ATCC 33970); SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58 / ATCC 33970; SOURCE 5 GENE: ATU1419; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: AGROBACTERIUM FABRUM STR. C58; SOURCE 10 ORGANISM_TAXID: 176299; SOURCE 11 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS REPRESSOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.MORERA,A.NARETTO,A.VIGOUROUX,P.LEGRAND REVDAT 4 24-JAN-24 6ZAB 1 REMARK REVDAT 3 20-JAN-21 6ZAB 1 JRNL REVDAT 2 23-DEC-20 6ZAB 1 JRNL REVDAT 1 02-DEC-20 6ZAB 0 JRNL AUTH A.VIGOUROUX,T.MEYER,A.NARETTO,P.LEGRAND,M.AUMONT-NICAISE, JRNL AUTH 2 A.DI CICCO,S.RENOUD,J.DORE,D.LEVY,L.VIAL,C.LAVIRE,S.MORERA JRNL TITL CHARACTERIZATION OF THE FIRST TETRAMERIC TRANSCRIPTION JRNL TITL 2 FACTOR OF THE GNTR SUPERFAMILY WITH ALLOSTERIC REGULATION JRNL TITL 3 FROM THE BACTERIAL PATHOGEN AGROBACTERIUM FABRUM. JRNL REF NUCLEIC ACIDS RES. V. 49 529 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33313837 JRNL DOI 10.1093/NAR/GKAA1181 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 70.8 REMARK 3 NUMBER OF REFLECTIONS : 16349 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 + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 817 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 40 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 16.40 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 409 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2618 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 390 REMARK 3 BIN R VALUE (WORKING SET) : 0.2596 REMARK 3 BIN FREE R VALUE : 0.3083 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.65 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1821 REMARK 3 NUCLEIC ACID ATOMS : 202 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 101.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.91990 REMARK 3 B22 (A**2) : 0.91990 REMARK 3 B33 (A**2) : -1.83980 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.380 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.304 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.222 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.300 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.222 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2107 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2883 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 737 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 345 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2107 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 273 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2468 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.01 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.22 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.46 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|73 - 502 } REMARK 3 ORIGIN FOR THE GROUP (A): -26.1280 70.5865 -18.0204 REMARK 3 T TENSOR REMARK 3 T11: -0.2423 T22: -0.1361 REMARK 3 T33: 0.2640 T12: -0.1019 REMARK 3 T13: 0.0989 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 3.3449 L22: 1.0064 REMARK 3 L33: 3.5334 L12: 0.8359 REMARK 3 L13: 1.2732 L23: 0.8453 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.2948 S13: -0.5301 REMARK 3 S21: 0.0188 S22: 0.0851 S23: -0.1703 REMARK 3 S31: 0.4430 S32: 0.3212 S33: -0.0862 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|6 - 72 } REMARK 3 ORIGIN FOR THE GROUP (A): -6.0875 90.4291 -9.4147 REMARK 3 T TENSOR REMARK 3 T11: -0.1850 T22: -0.0468 REMARK 3 T33: 0.0470 T12: 0.0587 REMARK 3 T13: -0.1559 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 8.8735 L22: 3.9051 REMARK 3 L33: 8.3155 L12: 0.7898 REMARK 3 L13: -3.3135 L23: -0.0817 REMARK 3 S TENSOR REMARK 3 S11: 0.2344 S12: 0.0738 S13: -0.6649 REMARK 3 S21: -0.4387 S22: -0.0891 S23: 0.1970 REMARK 3 S31: 0.1306 S32: -0.0218 S33: -0.1453 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 2.6567 104.2834 -15.6354 REMARK 3 T TENSOR REMARK 3 T11: -0.1208 T22: 0.1471 REMARK 3 T33: -0.1223 T12: -0.0728 REMARK 3 T13: 0.0551 T23: -0.0998 REMARK 3 L TENSOR REMARK 3 L11: 3.3586 L22: 6.9864 REMARK 3 L33: 4.3059 L12: -2.0028 REMARK 3 L13: -2.6184 L23: -1.2856 REMARK 3 S TENSOR REMARK 3 S11: 0.2061 S12: -0.2635 S13: 0.6229 REMARK 3 S21: 0.2431 S22: 0.0020 S23: -0.2688 REMARK 3 S31: -0.2586 S32: 0.4283 S33: -0.2081 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6Z74 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TERBUTANOL, NA-CITRATE, MGCL2, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 32.24667 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 64.49333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.24667 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 64.49333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.24667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 64.49333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 32.24667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 64.49333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.500000 0.866025 0.000000 -89.59000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 155.17443 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -32.24667 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 ARG A 2 REMARK 465 GLN A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 5 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: 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 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.2 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 ASP A 123 -30.79 -144.45 REMARK 500 ASP A 129 85.91 -67.54 REMARK 500 SER A 167 146.75 -37.91 REMARK 500 SER A 169 51.43 -92.05 REMARK 500 PHE A 171 37.52 -93.59 REMARK 500 ALA A 176 38.38 -75.97 REMARK 500 PRO A 237 104.70 -56.19 REMARK 500 SER A 243 59.52 -95.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA B 1 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 137 OD1 REMARK 620 2 HIS A 141 NE2 87.9 REMARK 620 3 HIS A 192 NE2 100.7 91.9 REMARK 620 4 HIS A 214 NE2 172.9 98.7 76.5 REMARK 620 5 CIT A 502 O7 84.9 103.4 163.9 96.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 DBREF 6ZAB A 1 244 UNP A9CJ36 A9CJ36_AGRFC 1 244 DBREF 6ZAB B 1 10 PDB 6ZAB 6ZAB 1 10 SEQADV 6ZAB HIS A 245 UNP A9CJ36 EXPRESSION TAG SEQADV 6ZAB HIS A 246 UNP A9CJ36 EXPRESSION TAG SEQADV 6ZAB HIS A 247 UNP A9CJ36 EXPRESSION TAG SEQADV 6ZAB HIS A 248 UNP A9CJ36 EXPRESSION TAG SEQADV 6ZAB HIS A 249 UNP A9CJ36 EXPRESSION TAG SEQADV 6ZAB HIS A 250 UNP A9CJ36 EXPRESSION TAG SEQRES 1 A 250 MET ARG GLN VAL ASP ALA ALA THR HIS GLY GLY ARG ALA SEQRES 2 A 250 VAL ILE GLU LEU ARG GLU LYS ILE LEU SER GLY GLU LEU SEQRES 3 A 250 PRO GLY GLY MET ARG LEU PHE GLU VAL SER THR ALA GLU SEQRES 4 A 250 LEU LEU ASP ILE SER ARG THR PRO VAL ARG GLU ALA LEU SEQRES 5 A 250 SER ARG LEU THR GLU GLU GLY LEU LEU ASN ARG LEU PRO SEQRES 6 A 250 GLY GLY GLY PHE VAL VAL ARG ARG PHE GLY PHE ALA ASP SEQRES 7 A 250 VAL VAL ASP ALA ILE GLU VAL ARG GLY VAL MET GLU GLY SEQRES 8 A 250 THR ALA ALA ARG LEU ALA ALA GLU ARG GLY VAL SER LYS SEQRES 9 A 250 VAL ALA LEU GLU GLU ILE ASP ALA THR VAL GLN GLN LEU SEQRES 10 A 250 ASP LEU CYS PHE GLY ASP ARG VAL ASP ASP VAL ASP PHE SEQRES 11 A 250 ASP GLY TYR ALA ALA LEU ASN ARG ILE PHE HIS HIS GLN SEQRES 12 A 250 LEU ALA ALA LEU CYS GLY SER GLU MET ILE ARG ARG GLU SEQRES 13 A 250 VAL GLU ARG ALA SER SER LEU PRO PHE ALA SER PRO SER SEQRES 14 A 250 ALA PHE LEU PRO ASP LYS ALA ASN ILE GLY ALA PHE ARG SEQRES 15 A 250 ARG SER LEU ARG GLY ALA GLN GLU GLN HIS LYS ALA ILE SEQRES 16 A 250 VAL ALA ALA ILE VAL ALA ARG GLU GLY ALA ARG ALA GLU SEQRES 17 A 250 ALA VAL ALA ARG GLU HIS SER ARG THR ALA ARG THR ASN SEQRES 18 A 250 LEU GLU TYR MET ILE ARG GLU ALA PRO GLU LEU ILE ALA SEQRES 19 A 250 GLN VAL PRO GLY LEU ALA LEU ILE SER ASP HIS HIS HIS SEQRES 20 A 250 HIS HIS HIS SEQRES 1 B 10 DA DT DG DT DA DT DA DC DA DT HET ZN A 501 1 HET CIT A 502 13 HET PEG A 503 7 HET EDO A 504 4 HETNAM ZN ZINC ION HETNAM CIT CITRIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN ZN 2+ FORMUL 4 CIT C6 H8 O7 FORMUL 5 PEG C4 H10 O3 FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *23(H2 O) HELIX 1 AA1 THR A 8 GLY A 24 1 17 HELIX 2 AA2 PHE A 33 ASP A 42 1 10 HELIX 3 AA3 SER A 44 GLU A 58 1 15 HELIX 4 AA4 GLY A 75 GLY A 101 1 27 HELIX 5 AA5 SER A 103 LEU A 119 1 17 HELIX 6 AA6 ASP A 129 CYS A 148 1 20 HELIX 7 AA7 SER A 150 SER A 161 1 12 HELIX 8 AA8 SER A 167 PHE A 171 5 5 HELIX 9 AA9 ARG A 183 ALA A 201 1 19 HELIX 10 AB1 GLU A 203 ALA A 229 1 27 HELIX 11 AB2 GLU A 231 VAL A 236 5 6 SHEET 1 AA1 3 ARG A 31 LEU A 32 0 SHEET 2 AA1 3 PHE A 69 VAL A 71 -1 O PHE A 69 N LEU A 32 SHEET 3 AA1 3 LEU A 61 ARG A 63 -1 N ASN A 62 O VAL A 70 LINK OD1 ASN A 137 ZN ZN A 501 1555 1555 2.12 LINK NE2 HIS A 141 ZN ZN A 501 1555 1555 2.35 LINK NE2 HIS A 192 ZN ZN A 501 1555 1555 2.28 LINK NE2 HIS A 214 ZN ZN A 501 1555 1555 2.38 LINK ZN ZN A 501 O7 CIT A 502 1555 1555 2.39 SITE 1 AC1 5 ASN A 137 HIS A 141 HIS A 192 HIS A 214 SITE 2 AC1 5 CIT A 502 SITE 1 AC2 13 ARG A 86 TYR A 133 ASN A 137 PRO A 168 SITE 2 AC2 13 PHE A 171 LEU A 185 ALA A 188 HIS A 214 SITE 3 AC2 13 SER A 215 THR A 217 ALA A 218 ASN A 221 SITE 4 AC2 13 ZN A 501 SITE 1 AC3 2 MET A 30 ASP A 42 SITE 1 AC4 3 PHE A 33 SER A 36 THR A 37 CRYST1 179.180 179.180 96.740 90.00 90.00 120.00 P 64 2 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 0.005581 0.003222 0.000000 0.00000 SCALE2 0.000000 0.006444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010337 0.00000