HEADER HYDROLASE/DNA 12-MAR-15 4YOQ TITLE CRYSTAL STRUCTURE OF MUTY BOUND TO ITS ANTI-SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: A/G-SPECIFIC ADENINE GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS 8-OXOGUANINE, BASE-EXCISION REPAIR, ANTI-SUBSTRATE, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.WANG,S.LEE,G.L.VERDINE REVDAT 4 27-SEP-23 4YOQ 1 SOURCE JRNL REMARK LINK REVDAT 3 22-JUL-15 4YOQ 1 JRNL REVDAT 2 03-JUN-15 4YOQ 1 JRNL REVDAT 1 27-MAY-15 4YOQ 0 JRNL AUTH L.WANG,S.J.LEE,G.L.VERDINE JRNL TITL STRUCTURAL BASIS FOR AVOIDANCE OF PROMUTAGENIC DNA REPAIR BY JRNL TITL 2 MUTY ADENINE DNA GLYCOSYLASE. JRNL REF J.BIOL.CHEM. V. 290 17096 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25995449 JRNL DOI 10.1074/JBC.M115.657866 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23608 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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 41.4152 - 4.5952 1.00 2669 142 0.1679 0.2182 REMARK 3 2 4.5952 - 3.6480 1.00 2531 137 0.1495 0.2120 REMARK 3 3 3.6480 - 3.1871 1.00 2479 129 0.1682 0.2486 REMARK 3 4 3.1871 - 2.8958 1.00 2489 118 0.1964 0.2523 REMARK 3 5 2.8958 - 2.6883 1.00 2460 143 0.2069 0.2941 REMARK 3 6 2.6883 - 2.5298 1.00 2472 126 0.2222 0.2937 REMARK 3 7 2.5298 - 2.4031 1.00 2460 142 0.2316 0.2861 REMARK 3 8 2.4031 - 2.2985 1.00 2435 139 0.2686 0.3296 REMARK 3 9 2.2985 - 2.2100 1.00 2397 140 0.3020 0.3821 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.62 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 : 0.010 3327 REMARK 3 ANGLE : 1.399 4609 REMARK 3 CHIRALITY : 0.081 498 REMARK 3 PLANARITY : 0.006 523 REMARK 3 DIHEDRAL : 19.617 1264 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 9:50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1490 87.6884 0.5544 REMARK 3 T TENSOR REMARK 3 T11: 0.3210 T22: 0.6237 REMARK 3 T33: 0.3730 T12: 0.0740 REMARK 3 T13: -0.0693 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 1.9136 L22: 3.8510 REMARK 3 L33: 3.8002 L12: 0.5771 REMARK 3 L13: -0.6126 L23: 0.9030 REMARK 3 S TENSOR REMARK 3 S11: 0.0900 S12: 1.2438 S13: 0.0522 REMARK 3 S21: -0.6275 S22: -0.1956 S23: 0.4747 REMARK 3 S31: 0.2622 S32: 0.0047 S33: 0.1025 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 51:105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0381 99.9742 15.8475 REMARK 3 T TENSOR REMARK 3 T11: 0.2990 T22: 0.2208 REMARK 3 T33: 0.4682 T12: -0.0143 REMARK 3 T13: -0.0120 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 1.8826 L22: 5.9826 REMARK 3 L33: 3.6470 L12: 0.6826 REMARK 3 L13: 0.1482 L23: -1.1184 REMARK 3 S TENSOR REMARK 3 S11: -0.1273 S12: 0.0132 S13: 0.9637 REMARK 3 S21: 0.4310 S22: 0.0079 S23: 0.2250 REMARK 3 S31: -0.6483 S32: 0.1188 S33: 0.0260 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 106:210 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0708 84.4421 -1.6293 REMARK 3 T TENSOR REMARK 3 T11: 0.3138 T22: 0.7226 REMARK 3 T33: 0.3014 T12: -0.0313 REMARK 3 T13: 0.0444 T23: -0.0301 REMARK 3 L TENSOR REMARK 3 L11: 3.4828 L22: 4.6386 REMARK 3 L33: 1.8504 L12: 0.5970 REMARK 3 L13: 0.3149 L23: 1.1669 REMARK 3 S TENSOR REMARK 3 S11: -0.0690 S12: 1.3679 S13: -0.3653 REMARK 3 S21: -0.5644 S22: 0.1125 S23: -0.4178 REMARK 3 S31: -0.1634 S32: 0.2119 S33: -0.0134 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 211:234 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2905 67.2102 0.0077 REMARK 3 T TENSOR REMARK 3 T11: 0.4492 T22: 0.8250 REMARK 3 T33: 0.9846 T12: 0.0202 REMARK 3 T13: 0.0197 T23: -0.6701 REMARK 3 L TENSOR REMARK 3 L11: 0.1106 L22: 3.3220 REMARK 3 L33: 4.6840 L12: 0.2655 REMARK 3 L13: -0.3002 L23: 2.5080 REMARK 3 S TENSOR REMARK 3 S11: -0.2821 S12: 0.6935 S13: -0.8373 REMARK 3 S21: -0.0837 S22: 0.0002 S23: -0.1231 REMARK 3 S31: 0.2617 S32: -0.1790 S33: -1.1565 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 235:360 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9853 92.9150 39.1431 REMARK 3 T TENSOR REMARK 3 T11: 0.7420 T22: 0.6929 REMARK 3 T33: 0.4282 T12: -0.0180 REMARK 3 T13: -0.1374 T23: -0.1279 REMARK 3 L TENSOR REMARK 3 L11: 2.7791 L22: 2.5802 REMARK 3 L33: 4.5319 L12: 0.1640 REMARK 3 L13: -0.0531 L23: -0.4629 REMARK 3 S TENSOR REMARK 3 S11: 0.0701 S12: -1.0397 S13: 0.5382 REMARK 3 S21: 1.1249 S22: 0.1752 S23: -0.4971 REMARK 3 S31: 0.0311 S32: 0.5439 S33: -0.1323 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9004 83.0632 14.6483 REMARK 3 T TENSOR REMARK 3 T11: 0.3441 T22: 0.5016 REMARK 3 T33: 0.6684 T12: 0.0175 REMARK 3 T13: 0.0618 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 5.4740 L22: 5.6183 REMARK 3 L33: 6.1272 L12: -5.5480 REMARK 3 L13: -5.7978 L23: 5.8659 REMARK 3 S TENSOR REMARK 3 S11: -0.5965 S12: -0.4050 S13: -0.7604 REMARK 3 S21: 0.3419 S22: 0.3905 S23: -1.0370 REMARK 3 S31: 0.8294 S32: 0.9905 S33: 0.1985 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN B AND RESID 7:11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4729 77.7821 21.2065 REMARK 3 T TENSOR REMARK 3 T11: 0.8297 T22: 0.4464 REMARK 3 T33: 0.9085 T12: -0.2317 REMARK 3 T13: -0.0430 T23: 0.0427 REMARK 3 L TENSOR REMARK 3 L11: 1.2473 L22: 3.8326 REMARK 3 L33: 2.9126 L12: -1.6701 REMARK 3 L13: -1.6554 L23: 1.1460 REMARK 3 S TENSOR REMARK 3 S11: -0.0471 S12: 0.0909 S13: -1.7956 REMARK 3 S21: -0.2216 S22: -0.1318 S23: 0.8351 REMARK 3 S31: 1.2902 S32: -1.0760 S33: 0.2460 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN C AND RESID 13:22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7270 80.6508 13.6076 REMARK 3 T TENSOR REMARK 3 T11: 0.5106 T22: 0.5813 REMARK 3 T33: 0.5175 T12: 0.0700 REMARK 3 T13: -0.0265 T23: 0.1378 REMARK 3 L TENSOR REMARK 3 L11: 7.0919 L22: 3.4498 REMARK 3 L33: 6.0626 L12: -0.0289 REMARK 3 L13: -0.6939 L23: 0.6228 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: -0.6456 S13: -0.7772 REMARK 3 S21: 0.2828 S22: -0.2270 S23: -0.4525 REMARK 3 S31: 1.3643 S32: 0.3937 S33: 0.2152 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 4YOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 142.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.52300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: PDB ENTRY 1RRQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 8.0, 250 MM NAOAC, 29% REMARK 280 (WT/VOL) PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 18.84850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.22850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.29700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.22850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.84850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.29700 REMARK 290 SMTRY3 4 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 PHE A 8 REMARK 465 LYS A 230 REMARK 465 LYS A 231 REMARK 465 THR A 232 REMARK 465 ALA A 233 REMARK 465 GLU A 288 REMARK 465 GLN A 289 REMARK 465 TYR A 290 REMARK 465 GLY A 291 REMARK 465 GLY A 361 REMARK 465 VAL A 362 REMARK 465 ARG A 363 REMARK 465 PRO A 364 REMARK 465 PRO A 365 REMARK 465 PRO A 366 REMARK 465 DT C 12 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 SER A 360 O REMARK 470 DG C 13 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 274 O HOH A 501 2.12 REMARK 500 O HOH A 592 O HOH A 595 2.13 REMARK 500 OE2 GLU A 78 O HOH A 502 2.13 REMARK 500 OD1 ASP A 77 O HOH A 503 2.17 REMARK 500 OP2 DT C 22 O HOH C 201 2.19 REMARK 500 NH2 ARG A 353 O HOH A 504 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 7 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DT B 7 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DG C 19 P - O5' - C5' ANGL. DEV. = -14.0 DEGREES REMARK 500 DT C 22 C4 - C5 - C7 ANGL. DEV. = 4.1 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 144 -161.93 -112.63 REMARK 500 ALA A 179 91.98 -68.44 REMARK 500 LEU A 262 50.78 39.73 REMARK 500 ASP A 274 79.57 54.69 REMARK 500 MET A 285 56.87 -61.48 REMARK 500 GLU A 328 -136.47 -139.68 REMARK 500 GLU A 329 -143.21 59.49 REMARK 500 ALA A 359 -7.06 -59.57 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 A 599 DISTANCE = 6.71 ANGSTROMS 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 LEU A 120 O 91.2 REMARK 620 3 VAL A 123 O 88.8 94.4 REMARK 620 4 DC C 21 OP1 173.7 84.4 87.0 REMARK 620 5 HOH C 205 O 93.8 174.8 87.1 90.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 401 S1 120.8 REMARK 620 3 SF4 A 401 S3 128.6 100.2 REMARK 620 4 SF4 A 401 S4 111.1 95.8 92.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 401 S2 136.1 REMARK 620 3 SF4 A 401 S3 103.5 95.1 REMARK 620 4 SF4 A 401 S4 121.7 96.0 93.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S1 122.9 REMARK 620 3 SF4 A 401 S2 124.1 94.2 REMARK 620 4 SF4 A 401 S4 117.1 96.5 95.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 401 S1 131.0 REMARK 620 3 SF4 A 401 S2 117.8 94.2 REMARK 620 4 SF4 A 401 S3 112.7 100.0 93.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YPR RELATED DB: PDB REMARK 900 RELATED ID: 4YPH RELATED DB: PDB DBREF 4YOQ A 1 366 UNP P83847 P83847_GEOSE 1 366 DBREF 4YOQ B 1 11 PDB 4YOQ 4YOQ 1 11 DBREF 4YOQ C 12 22 PDB 4YOQ 4YOQ 12 22 SEQADV 4YOQ GLY A -2 UNP P83847 EXPRESSION TAG SEQADV 4YOQ SER A -1 UNP P83847 EXPRESSION TAG SEQADV 4YOQ HIS A 0 UNP P83847 EXPRESSION TAG SEQADV 4YOQ ASP A 144 UNP P83847 ASN 144 ENGINEERED MUTATION SEQADV 4YOQ CYS A 164 UNP P83847 PRO 164 ENGINEERED MUTATION SEQRES 1 A 369 GLY SER HIS MET THR ARG GLU THR GLU ARG PHE PRO ALA SEQRES 2 A 369 ARG GLU PHE GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG SEQRES 3 A 369 GLU ARG ARG ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO SEQRES 4 A 369 TYR LYS VAL TRP VAL SER GLU VAL MET LEU GLN GLN THR SEQRES 5 A 369 ARG VAL GLU THR VAL ILE PRO TYR PHE GLU GLN PHE ILE SEQRES 6 A 369 ASP ARG PHE PRO THR LEU GLU ALA LEU ALA ASP ALA ASP SEQRES 7 A 369 GLU ASP GLU VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR SEQRES 8 A 369 TYR SER ARG VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU SEQRES 9 A 369 VAL LYS THR ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO SEQRES 10 A 369 ASP GLU PHE SER ARG LEU LYS GLY VAL GLY PRO TYR THR SEQRES 11 A 369 VAL GLY ALA VAL LEU SER LEU ALA TYR GLY VAL PRO GLU SEQRES 12 A 369 PRO ALA VAL ASP GLY ASN VAL MET ARG VAL LEU SER ARG SEQRES 13 A 369 LEU PHE LEU VAL THR ASP ASP ILE ALA LYS CYS SER THR SEQRES 14 A 369 ARG LYS ARG PHE GLU GLN ILE VAL ARG GLU ILE MET ALA SEQRES 15 A 369 TYR GLU ASN PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU SEQRES 16 A 369 LEU GLY ALA LEU VAL CYS THR PRO ARG ARG PRO SER CYS SEQRES 17 A 369 LEU LEU CYS PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA SEQRES 18 A 369 GLU GLY VAL ALA GLU GLU LEU PRO VAL LYS MET LYS LYS SEQRES 19 A 369 THR ALA VAL LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU SEQRES 20 A 369 ALA ASP ASP GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SEQRES 21 A 369 SER THR GLY LEU LEU ALA ASN LEU TRP GLU PHE PRO SER SEQRES 22 A 369 CYS GLU THR ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU SEQRES 23 A 369 GLN MET VAL GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU SEQRES 24 A 369 THR GLU PRO ILE VAL SER PHE GLU HIS ALA PHE SER HIS SEQRES 25 A 369 LEU VAL TRP GLN LEU THR VAL PHE PRO GLY ARG LEU VAL SEQRES 26 A 369 HIS GLY GLY PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO SEQRES 27 A 369 GLU ASP GLU LEU LYS ALA TYR ALA PHE PRO VAL SER HIS SEQRES 28 A 369 GLN ARG VAL TRP ARG GLU TYR LYS GLU TRP ALA SER GLY SEQRES 29 A 369 VAL ARG PRO PRO PRO SEQRES 1 B 11 DA DA DG DA DC 8OG DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA DC DG DT DC DT HET 8OG B 6 23 HET SF4 A 401 8 HET NA A 402 1 HET GOL C 101 6 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 SF4 FE4 S4 FORMUL 5 NA NA 1+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *127(H2 O) HELIX 1 AA1 PRO A 9 ARG A 25 1 17 HELIX 2 AA2 LEU A 28 LYS A 32 5 5 HELIX 3 AA3 ASP A 35 GLN A 47 1 13 HELIX 4 AA4 ARG A 50 PHE A 65 1 16 HELIX 5 AA5 THR A 67 ALA A 74 1 8 HELIX 6 AA6 ASP A 75 GLU A 84 1 10 HELIX 7 AA7 TYR A 89 TYR A 106 1 18 HELIX 8 AA8 ASP A 113 ARG A 119 1 7 HELIX 9 AA9 GLY A 124 GLY A 137 1 14 HELIX 10 AB1 ASP A 144 PHE A 155 1 12 HELIX 11 AB2 LYS A 163 MET A 178 1 16 HELIX 12 AB3 ASN A 182 VAL A 197 1 16 HELIX 13 AB4 VAL A 210 TYR A 213 5 4 HELIX 14 AB5 CYS A 214 GLY A 220 1 7 HELIX 15 AB6 VAL A 221 LEU A 225 5 5 HELIX 16 AB7 LYS A 279 MET A 285 1 7 HELIX 17 AB8 PRO A 335 TYR A 342 5 8 HELIX 18 AB9 PRO A 345 ALA A 359 1 15 SHEET 1 AA1 4 SER A 270 GLU A 272 0 SHEET 2 AA1 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA1 4 LEU A 310 VAL A 322 1 O VAL A 311 N VAL A 237 SHEET 4 AA1 4 GLN A 293 LEU A 296 -1 N GLN A 293 O VAL A 322 SHEET 1 AA2 4 SER A 270 GLU A 272 0 SHEET 2 AA2 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA2 4 LEU A 310 VAL A 322 1 O VAL A 311 N VAL A 237 SHEET 4 AA2 4 VAL A 301 ALA A 306 -1 N HIS A 305 O TRP A 312 SHEET 1 AA3 3 TRP A 266 GLU A 267 0 SHEET 2 AA3 3 VAL A 251 LYS A 255 -1 N ARG A 254 O GLU A 267 SHEET 3 AA3 3 TYR A 331 ALA A 334 -1 O ALA A 334 N VAL A 251 LINK O3' DC B 5 P 8OG B 6 1555 1555 1.60 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.61 LINK O SER A 118 NA NA A 402 1555 1555 2.33 LINK O LEU A 120 NA NA A 402 1555 1555 2.62 LINK O VAL A 123 NA NA A 402 1555 1555 2.44 LINK SG CYS A 198 FE2 SF4 A 401 1555 1555 2.45 LINK SG CYS A 205 FE1 SF4 A 401 1555 1555 2.46 LINK SG CYS A 208 FE3 SF4 A 401 1555 1555 2.43 LINK SG CYS A 214 FE4 SF4 A 401 1555 1555 2.48 LINK NA NA A 402 OP1 DC C 21 1555 1555 2.90 LINK NA NA A 402 O HOH C 205 1555 1555 2.28 CISPEP 1 LEU A 225 PRO A 226 0 -0.76 SITE 1 AC1 5 CYS A 198 CYS A 205 CYS A 208 CYS A 214 SITE 2 AC1 5 ALA A 222 SITE 1 AC2 5 SER A 118 LEU A 120 VAL A 123 DC C 21 SITE 2 AC2 5 HOH C 205 SITE 1 AC3 6 ALA A 162 DA B 2 DG B 3 DC C 18 SITE 2 AC3 6 DG C 19 DT C 20 CRYST1 37.697 84.594 142.457 90.00 90.00 90.00 P 21 21 21 4 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 0.026527 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007020 0.00000