HEADER LYASE 26-JUL-14 4U63 TITLE CRYSTAL STRUCTURE OF A BACTERIAL CLASS III PHOTOLYASE FROM TITLE 2 AGROBACTERIUM TUMEFACIENS AT 1.67A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PHOTOLYASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MRGSHHHHHHGSHVI - EXPRESSION TAQ SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58 / ATCC 33970; SOURCE 5 GENE: ATU1218; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1010810; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS PHOTOLYASE, DNA REPAIR, LYASE, METHENYLTETRAHYDROFOLATE, KEYWDS 2 CYCLOPYRIMIDINE DIMER, FLAVIN, FAD, FLAVOPROTEIN, PHOTOREDUCTION, KEYWDS 3 TRP TRIADE, DOUBLE-STRANDED, DNA DAMAGE, DNA, ULTRAVIOLET RAYS, KEYWDS 4 AGROBACTERIUM TUMEFACIENS EXPDTA X-RAY DIFFRACTION AUTHOR P.SCHEERER,F.ZHANG,J.KALMS,D.VON STETTEN,N.KRAUSS,I.OBERPICHLER, AUTHOR 2 T.LAMPARTER REVDAT 4 20-DEC-23 4U63 1 REMARK REVDAT 3 13-MAY-15 4U63 1 JRNL REVDAT 2 01-APR-15 4U63 1 JRNL REVDAT 1 25-MAR-15 4U63 0 JRNL AUTH P.SCHEERER,F.ZHANG,J.KALMS,D.VON STETTEN,N.KRAU, JRNL AUTH 2 I.OBERPICHLER,T.LAMPARTER JRNL TITL THE CLASS III CYCLOBUTANE PYRIMIDINE DIMER PHOTOLYASE JRNL TITL 2 STRUCTURE REVEALS A NEW ANTENNA CHROMOPHORE BINDING SITE AND JRNL TITL 3 ALTERNATIVE PHOTOREDUCTION PATHWAYS. JRNL REF J.BIOL.CHEM. V. 290 11504 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25784552 JRNL DOI 10.1074/JBC.M115.637868 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 84703 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4330 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6172 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 297 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 164 REMARK 3 SOLVENT ATOMS : 547 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : 0.87000 REMARK 3 B33 (A**2) : -2.82000 REMARK 3 B12 (A**2) : 0.43000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.115 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4231 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5800 ; 1.229 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -3 A 478 REMARK 3 ORIGIN FOR THE GROUP (A): 35.3708 -17.0159 -37.5860 REMARK 3 T TENSOR REMARK 3 T11: 0.0124 T22: 0.0059 REMARK 3 T33: 0.0640 T12: 0.0035 REMARK 3 T13: -0.0009 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.0533 L22: 0.0937 REMARK 3 L33: 0.0100 L12: 0.0175 REMARK 3 L13: 0.0187 L23: -0.0035 REMARK 3 S TENSOR REMARK 3 S11: -0.0015 S12: -0.0015 S13: 0.0009 REMARK 3 S21: -0.0116 S22: -0.0013 S23: 0.0073 REMARK 3 S31: -0.0039 S32: -0.0032 S33: 0.0028 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1001 B 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4178 -20.3485 -36.6257 REMARK 3 T TENSOR REMARK 3 T11: 0.1412 T22: 0.1121 REMARK 3 T33: 0.0410 T12: -0.0830 REMARK 3 T13: 0.0066 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 29.3776 L22: 9.6981 REMARK 3 L33: 22.5275 L12: 12.2532 REMARK 3 L13: 22.7864 L23: 11.8034 REMARK 3 S TENSOR REMARK 3 S11: 0.9704 S12: -1.5761 S13: -0.0163 REMARK 3 S21: 0.9612 S22: -0.8174 S23: 0.1800 REMARK 3 S31: 1.3274 S32: -1.5500 S33: -0.1530 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1002 C 1002 REMARK 3 ORIGIN FOR THE GROUP (A): 37.8533 -14.6007 -32.0403 REMARK 3 T TENSOR REMARK 3 T11: 0.0205 T22: 0.0069 REMARK 3 T33: 0.0583 T12: 0.0058 REMARK 3 T13: -0.0009 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.6130 L22: 2.8320 REMARK 3 L33: 0.0479 L12: 0.6335 REMARK 3 L13: -0.1677 L23: -0.2390 REMARK 3 S TENSOR REMARK 3 S11: -0.0050 S12: 0.0067 S13: -0.0051 REMARK 3 S21: 0.0488 S22: 0.0057 S23: 0.0247 REMARK 3 S31: -0.0015 S32: -0.0020 S33: -0.0007 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1001 D 1014 REMARK 3 ORIGIN FOR THE GROUP (A): 42.0903 -12.1645 -41.0314 REMARK 3 T TENSOR REMARK 3 T11: 0.0952 T22: 0.0542 REMARK 3 T33: 0.1229 T12: 0.0333 REMARK 3 T13: -0.0432 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.1571 L22: 0.2042 REMARK 3 L33: 0.2439 L12: -0.0293 REMARK 3 L13: 0.0205 L23: 0.2097 REMARK 3 S TENSOR REMARK 3 S11: -0.0193 S12: -0.0776 S13: -0.0985 REMARK 3 S21: 0.0242 S22: -0.0052 S23: 0.0726 REMARK 3 S31: 0.0511 S32: -0.0245 S33: 0.0245 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 547 REMARK 3 ORIGIN FOR THE GROUP (A): 37.6745 -17.3880 -38.6462 REMARK 3 T TENSOR REMARK 3 T11: 0.0197 T22: 0.0087 REMARK 3 T33: 0.0739 T12: 0.0068 REMARK 3 T13: -0.0043 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.0856 L22: 0.1643 REMARK 3 L33: 0.1416 L12: -0.0034 REMARK 3 L13: -0.0212 L23: -0.0637 REMARK 3 S TENSOR REMARK 3 S11: -0.0019 S12: -0.0185 S13: 0.0020 REMARK 3 S21: -0.0156 S22: 0.0008 S23: 0.0060 REMARK 3 S31: 0.0099 S32: -0.0091 S33: 0.0011 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 1 REMARK 3 ORIGIN FOR THE GROUP (A): 18.2901 -8.9900 -44.6567 REMARK 3 T TENSOR REMARK 3 T11: 0.0900 T22: 0.0873 REMARK 3 T33: 0.1419 T12: 0.0043 REMARK 3 T13: -0.0029 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 4.8660 L22: 8.7364 REMARK 3 L33: 18.0404 L12: -3.0404 REMARK 3 L13: 3.6427 L23: 7.9558 REMARK 3 S TENSOR REMARK 3 S11: 0.1116 S12: 0.1464 S13: -0.0860 REMARK 3 S21: -0.1503 S22: -0.2682 S23: 0.1968 REMARK 3 S31: -0.0414 S32: -0.1573 S33: 0.1567 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4U63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918420 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89158 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.93000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: 1U3C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 M AMMONIUM SULFATE, 10% (V/V) REMARK 280 GLYCEROL, 75 MM SODIUM CHLORIDE, 12.5 MM TRIS (HYDROXYMETHYL) REMARK 280 AMINO METHANE, 1.25 MM ETHYLENEDIAMINETETRAACETIC ACID., PH 7.8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -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 130.63467 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 65.31733 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 65.31733 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 130.63467 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -154.0 KCAL/MOL 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 -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 VAL A -5 REMARK 465 ILE A -4 REMARK 465 THR A 479 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 LYS A 42 CG CD CE NZ REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 LYS A 193 CG CD CE NZ REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 LYS A 440 CG CD CE NZ REMARK 470 ASP A 441 CG OD1 OD2 REMARK 470 LYS A 444 CG CD CE NZ REMARK 470 LYS A 452 CG CD CE NZ REMARK 470 LYS A 477 CG CD CE NZ 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 13 -92.58 -130.73 REMARK 500 LYS A 14 59.46 -114.75 REMARK 500 ASP A 15 48.07 -148.87 REMARK 500 GLU A 161 135.95 -37.67 REMARK 500 THR A 192 -81.08 -113.85 REMARK 500 ASP A 411 53.89 -143.84 REMARK 500 LYS A 452 -67.78 -131.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1363 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A1522 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1544 DISTANCE = 5.99 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MHF A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1016 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 1017 DBREF 4U63 A 2 479 UNP A9CJC9 A9CJC9_AGRT5 2 479 SEQADV 4U63 MET A -18 UNP A9CJC9 INITIATING METHIONINE SEQADV 4U63 ARG A -17 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 GLY A -16 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 SER A -15 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -14 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -13 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -12 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -11 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -10 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -9 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 GLY A -8 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 SER A -7 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 HIS A -6 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 VAL A -5 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 ILE A -4 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 SER A -3 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 SER A -2 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 ILE A -1 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 ALA A 0 UNP A9CJC9 EXPRESSION TAG SEQADV 4U63 SER A 1 UNP A9CJC9 EXPRESSION TAG SEQRES 1 A 498 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER HIS SEQRES 2 A 498 VAL ILE SER SER ILE ALA SER SER LEU LYS THR ALA PRO SEQRES 3 A 498 VAL ILE VAL TRP PHE ARG LYS ASP LEU ARG LEU SER ASP SEQRES 4 A 498 ASN LEU ALA LEU LEU ALA ALA VAL GLU HIS GLY GLY PRO SEQRES 5 A 498 VAL ILE PRO VAL TYR ILE ARG GLU LYS SER ALA GLY PRO SEQRES 6 A 498 LEU GLY GLY ALA GLN GLU TRP TRP LEU HIS HIS SER LEU SEQRES 7 A 498 ALA ALA LEU SER SER SER LEU GLU LYS ALA GLY GLY ARG SEQRES 8 A 498 LEU VAL LEU ALA SER GLY ASP ALA GLU ARG ILE LEU ARG SEQRES 9 A 498 ASP LEU ILE SER GLU THR GLY ALA ASP THR VAL VAL TRP SEQRES 10 A 498 ASN ARG ARG TYR ASP PRO THR GLY MET ALA THR ASP LYS SEQRES 11 A 498 ALA LEU LYS GLN LYS LEU ARG ASP ASP GLY LEU THR VAL SEQRES 12 A 498 ARG SER PHE SER GLY GLN LEU LEU HIS GLU PRO SER ARG SEQRES 13 A 498 LEU GLN THR LYS SER GLY GLY PRO TYR ARG VAL TYR THR SEQRES 14 A 498 PRO PHE TRP ARG ALA LEU GLU GLY SER ASP GLU PRO HIS SEQRES 15 A 498 ALA PRO ALA ASP PRO PRO LYS SER LEU THR ALA PRO LYS SEQRES 16 A 498 VAL TRP PRO LYS SER GLU LYS LEU SER ASN TRP LYS LEU SEQRES 17 A 498 LEU PRO THR LYS PRO ASP TRP ALA LYS ASP PHE SER ASP SEQRES 18 A 498 ILE TRP THR PRO GLY GLU THR GLY ALA LEU ASP LYS LEU SEQRES 19 A 498 ASP ASP PHE ILE ASP GLY ALA LEU LYS GLY TYR GLU GLU SEQRES 20 A 498 GLY ARG ASP PHE PRO ALA LYS PRO ALA THR SER LEU LEU SEQRES 21 A 498 SER PRO HIS LEU ALA ALA GLY GLU ILE SER PRO ALA ALA SEQRES 22 A 498 VAL TRP HIS ALA THR LYS GLY LEU SER ARG HIS ILE ALA SEQRES 23 A 498 SER ASN ASP ILE SER ARG PHE ARG LYS GLU ILE VAL TRP SEQRES 24 A 498 ARG GLU PHE CYS TYR HIS LEU LEU PHE HIS PHE PRO GLU SEQRES 25 A 498 LEU GLY GLU LYS ASN TRP ASN ASP SER PHE ASP ALA PHE SEQRES 26 A 498 SER TRP ARG ASP ASP GLU LYS SER PHE LYS ALA TRP THR SEQRES 27 A 498 ARG GLY MET THR GLY TYR PRO ILE VAL ASP ALA GLY MET SEQRES 28 A 498 ARG GLN LEU TRP GLN HIS GLY THR MET HIS ASN ARG VAL SEQRES 29 A 498 ARG MET ILE VAL ALA SER PHE LEU ILE LYS HIS LEU LEU SEQRES 30 A 498 ILE ASP TRP ARG LYS GLY GLU LYS TRP PHE ARG ASP THR SEQRES 31 A 498 LEU VAL ASP ALA ASP PRO ALA SER ASN ALA ALA ASN TRP SEQRES 32 A 498 GLN TRP VAL ALA GLY SER GLY ALA ASP ALA SER PRO PHE SEQRES 33 A 498 PHE ARG ILE PHE ASN PRO ILE LEU GLN GLY GLU LYS PHE SEQRES 34 A 498 ASP GLY ASP GLY ASP TYR VAL ARG ARG PHE VAL PRO GLU SEQRES 35 A 498 LEU GLU LYS LEU GLU ARG LYS TYR ILE HIS LYS PRO PHE SEQRES 36 A 498 GLU ALA PRO LYS ASP ALA LEU LYS LYS ALA GLY VAL GLU SEQRES 37 A 498 LEU GLY LYS THR TYR PRO LEU PRO ILE VAL ASP HIS GLY SEQRES 38 A 498 LYS ALA ARG GLU ARG ALA LEU ALA ALA TYR ALA ALA VAL SEQRES 39 A 498 LYS LYS THR THR HET MHF A1001 33 HET FAD A1002 53 HET SO4 A1003 5 HET SO4 A1004 5 HET SO4 A1005 5 HET SO4 A1006 5 HET SO4 A1007 5 HET SO4 A1008 5 HET SO4 A1009 5 HET SO4 A1010 5 HET SO4 A1011 5 HET SO4 A1012 5 HET SO4 A1013 5 HET SO4 A1014 5 HET SO4 A1015 5 HET SO4 A1016 5 HET TRS A1017 8 HETNAM MHF 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 MHF C20 H23 N7 O6 FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 SO4 14(O4 S 2-) FORMUL 18 TRS C4 H12 N O3 1+ FORMUL 19 HOH *547(H2 O) HELIX 1 AA1 ASN A 21 GLY A 31 1 11 HELIX 2 AA2 GLY A 48 ALA A 69 1 22 HELIX 3 AA3 ASP A 79 GLY A 92 1 14 HELIX 4 AA4 ASP A 103 ASP A 120 1 18 HELIX 5 AA5 VAL A 148 SER A 159 1 12 HELIX 6 AA6 LYS A 183 LYS A 188 5 6 HELIX 7 AA7 ASP A 199 TRP A 204 1 6 HELIX 8 AA8 GLY A 207 ASP A 220 1 14 HELIX 9 AA9 GLY A 225 ARG A 230 1 6 HELIX 10 AB1 LEU A 241 ALA A 247 1 7 HELIX 11 AB2 SER A 251 ALA A 258 1 8 HELIX 12 AB3 ALA A 267 PHE A 291 1 25 HELIX 13 AB4 ASN A 300 ASP A 304 5 5 HELIX 14 AB5 ASP A 311 ARG A 320 1 10 HELIX 15 AB6 TYR A 325 GLY A 339 1 15 HELIX 16 AB7 HIS A 342 LYS A 355 1 14 HELIX 17 AB8 ASP A 360 LEU A 372 1 13 HELIX 18 AB9 ALA A 378 GLY A 389 1 12 HELIX 19 AC1 ASN A 402 ASP A 411 1 10 HELIX 20 AC2 GLY A 414 VAL A 421 1 8 HELIX 21 AC3 PRO A 422 GLU A 425 5 4 HELIX 22 AC4 GLU A 428 HIS A 433 1 6 HELIX 23 AC5 LYS A 434 ALA A 438 5 5 HELIX 24 AC6 PRO A 439 GLY A 447 1 9 HELIX 25 AC7 ASP A 460 LYS A 477 1 18 SHEET 1 AA1 5 VAL A 74 SER A 77 0 SHEET 2 AA1 5 VAL A 34 ARG A 40 1 N ARG A 40 O ALA A 76 SHEET 3 AA1 5 VAL A 8 PHE A 12 1 N PHE A 12 O VAL A 37 SHEET 4 AA1 5 THR A 95 ASN A 99 1 O VAL A 97 N ILE A 9 SHEET 5 AA1 5 THR A 123 PHE A 127 1 O THR A 123 N VAL A 96 CISPEP 1 LYS A 193 PRO A 194 0 -2.84 SITE 1 AC1 12 PRO A 194 TRP A 196 PHE A 200 ARG A 320 SITE 2 AC1 12 LEU A 335 TRP A 336 GLY A 339 ASP A 370 SITE 3 AC1 12 THR A 371 HOH A1111 HOH A1179 HOH A1308 SITE 1 AC2 32 TYR A 226 ARG A 230 THR A 238 SER A 239 SITE 2 AC2 32 LEU A 240 LEU A 241 SER A 242 LEU A 245 SITE 3 AC2 32 PHE A 274 GLU A 277 ILE A 278 ARG A 281 SITE 4 AC2 32 CYS A 284 MET A 341 ASN A 343 ARG A 346 SITE 5 AC2 32 MET A 347 PHE A 368 LEU A 372 ASP A 374 SITE 6 AC2 32 ALA A 375 ASP A 376 SER A 379 ASN A 380 SITE 7 AC2 32 ASN A 383 TRP A 384 HOH A1205 HOH A1218 SITE 8 AC2 32 HOH A1241 HOH A1248 HOH A1318 HOH A1437 SITE 1 AC3 3 ARG A 100 SER A 128 ARG A 137 SITE 1 AC4 9 ARG A 100 LYS A 114 ARG A 118 ARG A 125 SITE 2 AC4 9 SER A 126 HOH A1339 HOH A1407 HOH A1427 SITE 3 AC4 9 HOH A1553 SITE 1 AC5 4 ARG A 273 LYS A 276 HOH A1327 HOH A1542 SITE 1 AC6 6 TRP A 153 ARG A 154 LYS A 276 HOH A1303 SITE 2 AC6 6 HOH A1462 HOH A1542 SITE 1 AC7 2 ARG A 72 HOH A1494 SITE 1 AC8 4 LYS A 260 GLY A 261 ARG A 275 HOH A1498 SITE 1 AC9 5 SER A 263 ARG A 264 LYS A 297 HOH A1102 SITE 2 AC9 5 HOH A1152 SITE 1 AD1 5 GLY A 412 ASP A 413 ARG A 429 HOH A1263 SITE 2 AD1 5 HOH A1555 SITE 1 AD2 5 THR A 5 GLY A 31 GLY A 32 HOH A1533 SITE 2 AD2 5 HOH A1538 SITE 1 AD3 1 ARG A 309 SITE 1 AD4 5 LYS A 183 LEU A 184 SER A 185 HOH A1470 SITE 2 AD4 5 HOH A1595 SITE 1 AD5 2 ASP A 79 ARG A 82 SITE 1 AD6 6 HIS A 57 TRP A 204 THR A 205 PRO A 206 SITE 2 AD6 6 TRS A1017 HOH A1267 SITE 1 AD7 3 TRP A 386 ASP A 393 HOH A1391 SITE 1 AD8 10 TRP A 53 HIS A 57 LEU A 190 ASP A 195 SITE 2 AD8 10 ALA A 197 SO4 A1015 HOH A1264 HOH A1332 SITE 3 AD8 10 HOH A1646 HOH A1647 CRYST1 81.867 81.867 195.952 90.00 90.00 120.00 P 32 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 0.012215 0.007052 0.000000 0.00000 SCALE2 0.000000 0.014105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005103 0.00000