PDB Short entry for 3T79 HEADER DNA BINDING PROTEIN/DNA 29-JUL-11 3T79 TITLE NDC10: A PLATFORM FOR INNER KINETOCHORE ASSEMBLY IN BUDDING YEAST COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)- COMPND 3 3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CENTROMERIC CDEIII DNA; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: CENTROMERIC CDEIII DNA; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3'); COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: CENTROMERIC CDEIII DNA; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)- COMPND 20 3'); COMPND 21 CHAIN: F; COMPND 22 ENGINEERED: YES; COMPND 23 OTHER_DETAILS: CENTROMERIC CDEIII DNA; COMPND 24 MOL_ID: 5; COMPND 25 MOLECULE: KLLA0E03807P; COMPND 26 CHAIN: A, D; COMPND 27 FRAGMENT: DNA BINDING DOMAIN (RESIDUES 1-402); COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 10 MOL_ID: 4; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 13 MOL_ID: 5; SOURCE 14 ORGANISM_SCIENTIFIC: KLUYVEROMYCES LACTIS; SOURCE 15 ORGANISM_COMMON: YEAST; SOURCE 16 ORGANISM_TAXID: 284590; SOURCE 17 STRAIN: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / SOURCE 18 WM37; SOURCE 19 GENE: KLLA0E03807G; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS DNA RECOMBINASE, DNA BINDING, DNA, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.S.CHO,S.C.HARRISON REVDAT 4 13-SEP-23 3T79 1 REMARK REVDAT 3 18-JAN-12 3T79 1 JRNL REVDAT 2 28-DEC-11 3T79 1 JRNL REVDAT 1 07-DEC-11 3T79 0 JRNL AUTH U.S.CHO,S.C.HARRISON JRNL TITL NDC10 IS A PLATFORM FOR INNER KINETOCHORE ASSEMBLY IN JRNL TITL 2 BUDDING YEAST. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 48 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 22139014 JRNL DOI 10.1038/NSMB.2178 REMARK 2 REMARK 2 RESOLUTION. 3.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 3.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 13773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.289 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.331 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 686 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 43.6485 - 6.1706 0.97 2692 152 0.2473 0.3006 REMARK 3 2 6.1706 - 4.8999 0.99 2626 130 0.3008 0.3730 REMARK 3 3 4.8999 - 4.2811 0.99 2620 130 0.2767 0.3022 REMARK 3 4 4.2811 - 3.8900 0.99 2588 136 0.3006 0.3550 REMARK 3 5 3.8900 - 3.6113 0.99 2561 138 0.3817 0.3843 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 66.93 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.980 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 29.63880 REMARK 3 B22 (A**2) : -59.64940 REMARK 3 B33 (A**2) : 23.62940 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 : 0.009 7930 REMARK 3 ANGLE : 1.466 11029 REMARK 3 CHIRALITY : 0.084 1234 REMARK 3 PLANARITY : 0.007 1183 REMARK 3 DIHEDRAL : 21.759 3004 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:100) REMARK 3 ORIGIN FOR THE GROUP (A): -36.1201 -14.0622 -48.4529 REMARK 3 T TENSOR REMARK 3 T11: 1.0129 T22: 0.7689 REMARK 3 T33: 0.5510 T12: -0.0470 REMARK 3 T13: -0.1477 T23: -0.1336 REMARK 3 L TENSOR REMARK 3 L11: 0.3012 L22: 0.7495 REMARK 3 L33: -0.0156 L12: -0.2970 REMARK 3 L13: 0.2864 L23: -0.6357 REMARK 3 S TENSOR REMARK 3 S11: 0.1757 S12: -0.2215 S13: 0.1237 REMARK 3 S21: -0.2386 S22: 0.0314 S23: 0.0877 REMARK 3 S31: -0.2567 S32: -0.0564 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 101:402) REMARK 3 ORIGIN FOR THE GROUP (A): -24.4218 14.2893 -24.4512 REMARK 3 T TENSOR REMARK 3 T11: 0.4208 T22: 0.6418 REMARK 3 T33: 0.6296 T12: 0.0755 REMARK 3 T13: -0.1084 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.0553 L22: 1.1921 REMARK 3 L33: 1.0285 L12: 1.1645 REMARK 3 L13: 0.0650 L23: 0.2665 REMARK 3 S TENSOR REMARK 3 S11: -0.0458 S12: 0.1975 S13: 0.2865 REMARK 3 S21: -0.5276 S22: 0.0437 S23: 0.0865 REMARK 3 S31: 0.1062 S32: -0.2045 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESSEQ 1:100) REMARK 3 ORIGIN FOR THE GROUP (A): -66.5266 18.8110 -28.6743 REMARK 3 T TENSOR REMARK 3 T11: 0.7380 T22: 0.6978 REMARK 3 T33: 0.8316 T12: -0.0640 REMARK 3 T13: -0.3804 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.4840 L22: 0.0976 REMARK 3 L33: 0.4150 L12: 0.0207 REMARK 3 L13: 0.3031 L23: -0.0207 REMARK 3 S TENSOR REMARK 3 S11: 0.1808 S12: 0.4013 S13: 0.1147 REMARK 3 S21: -1.6852 S22: -0.4098 S23: -0.0724 REMARK 3 S31: 0.0855 S32: 0.2147 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESSEQ 101:402) REMARK 3 ORIGIN FOR THE GROUP (A): -49.4454 -9.6198 -8.3811 REMARK 3 T TENSOR REMARK 3 T11: 0.7762 T22: 0.6845 REMARK 3 T33: 0.5922 T12: -0.0050 REMARK 3 T13: -0.0512 T23: -0.0545 REMARK 3 L TENSOR REMARK 3 L11: -0.3652 L22: 0.5422 REMARK 3 L33: -0.2887 L12: 0.7636 REMARK 3 L13: -0.3500 L23: -1.2267 REMARK 3 S TENSOR REMARK 3 S11: 0.0388 S12: 0.2383 S13: -0.2365 REMARK 3 S21: -0.4476 S22: -0.1002 S23: 0.6847 REMARK 3 S31: 0.1671 S32: -0.0967 S33: -0.0000 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 3T79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 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) : 0.97914 REMARK 200 MONOCHROMATOR : CHOZU HLD8-24 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13821 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 22.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.22300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.91200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3SQI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 10,000, 0.1 M TRIS-HCL, PH8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 46.53000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.95750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.82550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.95750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.53000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.82550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, E, F, A, D 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, D 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 LEU A 36 REMARK 465 THR A 37 REMARK 465 GLY A 38 REMARK 465 ALA A 39 REMARK 465 ASP A 283 REMARK 465 SER A 284 REMARK 465 SER A 285 REMARK 465 GLU A 286 REMARK 465 ASN A 287 REMARK 465 THR A 288 REMARK 465 SER A 289 REMARK 465 THR A 290 REMARK 465 LEU A 291 REMARK 465 ALA A 292 REMARK 465 LEU D 36 REMARK 465 THR D 37 REMARK 465 GLY D 38 REMARK 465 ALA D 39 REMARK 465 ASP D 283 REMARK 465 SER D 284 REMARK 465 SER D 285 REMARK 465 GLU D 286 REMARK 465 ASN D 287 REMARK 465 THR D 288 REMARK 465 SER D 289 REMARK 465 THR D 290 REMARK 465 LEU D 291 REMARK 465 ALA D 292 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 D 383 OG SER D 386 1.65 REMARK 500 OE1 GLU D 81 OD1 ASN D 83 1.92 REMARK 500 OP2 DT F 8 NE ARG D 244 1.96 REMARK 500 O ARG A 244 OG1 THR A 247 1.98 REMARK 500 O LEU A 86 NE2 GLN A 90 2.06 REMARK 500 OD1 ASN D 148 NH1 ARG D 312 2.06 REMARK 500 NZ LYS A 162 O LEU A 228 2.09 REMARK 500 NH1 ARG D 156 O TRP D 268 2.09 REMARK 500 OG SER D 114 NE2 GLN D 144 2.10 REMARK 500 O LEU D 86 NE2 GLN D 90 2.10 REMARK 500 ND1 HIS A 389 O ASN D 105 2.11 REMARK 500 NZ LYS D 162 O GLU D 229 2.12 REMARK 500 OP2 DT C 4 NZ LYS A 128 2.16 REMARK 500 O LYS D 112 ND2 ASN D 116 2.17 REMARK 500 NZ LYS A 112 O CYS A 259 2.18 REMARK 500 NE ARG A 235 O LEU A 239 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 170 NE2 GLN D 320 3454 1.87 REMARK 500 O VAL A 321 OD2 ASP D 170 3454 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT C 4 C5' DT C 4 C4' 0.057 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 DT B 1 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DT B 1 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 2 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 2 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 3 O5' - C5' - C4' ANGL. DEV. = -9.5 DEGREES REMARK 500 DA C 3 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DA C 3 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 DA C 3 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT C 4 C5' - C4' - C3' ANGL. DEV. = 10.8 DEGREES REMARK 500 DT C 4 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT C 4 C6 - N1 - C2 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT C 4 C5 - C6 - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 8 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA C 15 O5' - C5' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DA E 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT E 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT E 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA E 7 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA E 7 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DA E 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA F 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA F 2 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DA F 2 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DA F 3 O4' - C4' - C3' ANGL. DEV. = -6.0 DEGREES REMARK 500 DT F 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT F 7 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT F 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT F 8 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 DT F 8 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA F 9 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT F 10 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT F 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA F 13 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA F 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 LEU A 11 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LYS A 128 CD - CE - NZ ANGL. DEV. = -17.3 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 LEU A 41 -85.07 -119.28 REMARK 500 SER A 181 -165.37 -79.62 REMARK 500 PHE A 210 -64.51 -99.49 REMARK 500 TYR A 216 -67.32 -135.38 REMARK 500 SER A 226 -62.66 -100.54 REMARK 500 GLN A 227 -9.97 -56.69 REMARK 500 PRO A 279 -176.74 -60.71 REMARK 500 THR A 299 -76.24 -105.92 REMARK 500 ILE A 300 -75.48 -94.97 REMARK 500 VAL A 355 -61.28 -93.04 REMARK 500 PHE A 356 71.21 -116.41 REMARK 500 GLU A 385 -7.05 -58.78 REMARK 500 LEU D 41 -78.98 -126.63 REMARK 500 SER D 75 -73.25 -47.64 REMARK 500 ASN D 105 -66.60 -102.90 REMARK 500 ARG D 209 -62.32 -94.17 REMARK 500 LYS D 215 -6.50 85.09 REMARK 500 SER D 226 -61.18 -104.81 REMARK 500 THR D 299 -74.13 -108.61 REMARK 500 ILE D 300 -72.93 -93.89 REMARK 500 VAL D 355 -62.26 -95.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SQI RELATED DB: PDB DBREF 3T79 A 1 402 UNP Q6CPM4 Q6CPM4_KLULA 1 402 DBREF 3T79 D 1 402 UNP Q6CPM4 Q6CPM4_KLULA 1 402 DBREF 3T79 B 1 15 PDB 3T79 3T79 1 15 DBREF 3T79 C 1 15 PDB 3T79 3T79 1 15 DBREF 3T79 E 1 14 PDB 3T79 3T79 1 14 DBREF 3T79 F 0 14 PDB 3T79 3T79 0 14 SEQRES 1 B 15 DT DT DA DA DT DT DT DA DT DA DA DA DA SEQRES 2 B 15 DT DT SEQRES 1 C 15 DA DA DA DT DT DT DT DA DT DA DA DA DT SEQRES 2 C 15 DT DA SEQRES 1 E 14 DT DA DA DT DT DT DA DT DA DA DA DA DT SEQRES 2 E 14 DT SEQRES 1 F 15 DA DA DA DA DA DT DT DT DT DA DT DA DA SEQRES 2 F 15 DA DT SEQRES 1 A 402 MET SER LYS LEU ASP SER LEU LEU LYS GLU LEU PRO THR SEQRES 2 A 402 ARG THR ALA HIS LEU TYR ARG SER ILE TRP HIS LYS TYR SEQRES 3 A 402 THR GLU TRP LEU LYS THR MET PRO ASP LEU THR GLY ALA SEQRES 4 A 402 ASP LEU LYS LEU PHE LEU SER GLN LYS TYR ILE VAL LYS SEQRES 5 A 402 TYR ILE ALA SER HIS ASP ASP ILE ALA LYS ASP PRO LEU SEQRES 6 A 402 PRO THR CYS ASP ALA MET ILE TRP PHE SER ARG ALA LEU SEQRES 7 A 402 ASP ILE GLU ASN ASN ASP VAL LEU VAL LEU GLN GLN ARG SEQRES 8 A 402 LEU TYR GLY LEU VAL LYS LEU LEU GLU PHE ASP TYR SER SEQRES 9 A 402 ASN VAL ILE ALA ILE LEU GLN LYS ILE SER ILE ASN LEU SEQRES 10 A 402 TRP ASN PRO SER THR ASP SER LEU GLN SER LYS HIS PHE SEQRES 11 A 402 LYS THR CYS GLN ASP LYS LEU LYS LEU LEU LEU ASP PHE SEQRES 12 A 402 GLN TRP LYS PHE ASN THR ASN VAL SER PHE GLU ASP ARG SEQRES 13 A 402 THR THR VAL SER LEU LYS ASP LEU GLN CYS ILE LEU ASP SEQRES 14 A 402 ASP GLU ASN GLY LYS CYS GLY LEU ALA HIS SER SER LYS SEQRES 15 A 402 PRO ASN PHE VAL LEU VAL PRO ASN PHE GLN SER PRO PHE SEQRES 16 A 402 THR CYS PRO ILE PHE THR MET ALA VAL TYR TYR TYR LEU SEQRES 17 A 402 ARG PHE HIS GLY VAL LYS LYS TYR TYR LYS GLY ASP GLY SEQRES 18 A 402 TYR GLN ILE LEU SER GLN LEU GLU HIS ILE PRO ILE ILE SEQRES 19 A 402 ARG GLY LYS SER LEU ASP GLN TYR PRO ARG GLU LEU THR SEQRES 20 A 402 LEU GLY ASN TRP TYR PRO THR ILE PHE LYS TYR CYS GLN SEQRES 21 A 402 LEU PRO TYR THR LYS LYS HIS TRP PHE GLN VAL ASN GLN SEQRES 22 A 402 GLU TRP PRO GLN PHE PRO ASP PHE SER ASP SER SER GLU SEQRES 23 A 402 ASN THR SER THR LEU ALA GLU SER ASP SER GLU ASN THR SEQRES 24 A 402 ILE GLY ILE PRO ASP PHE TYR ILE GLU LYS MET ASN ARG SEQRES 25 A 402 THR LYS LEU GLN PRO CYS PRO GLN VAL HIS VAL HIS LEU SEQRES 26 A 402 PHE PRO THR ASP LEU PRO PRO ASP ILE GLN ALA VAL PHE SEQRES 27 A 402 ASP LEU LEU ASN SER VAL LEU VAL THR SER LEU PRO LEU SEQRES 28 A 402 LEU TYR ARG VAL PHE PRO THR HIS ASP ILE PHE LEU ASP SEQRES 29 A 402 PRO SER LEU LYS THR PRO GLN ASN ILE ALA PHE LEU THR SEQRES 30 A 402 GLY THR LEU PRO LEU ASP ILE GLU SER GLN GLU HIS LEU SEQRES 31 A 402 LEU ALA GLN LEU ILE ASP LYS THR GLY THR VAL SER SEQRES 1 D 402 MET SER LYS LEU ASP SER LEU LEU LYS GLU LEU PRO THR SEQRES 2 D 402 ARG THR ALA HIS LEU TYR ARG SER ILE TRP HIS LYS TYR SEQRES 3 D 402 THR GLU TRP LEU LYS THR MET PRO ASP LEU THR GLY ALA SEQRES 4 D 402 ASP LEU LYS LEU PHE LEU SER GLN LYS TYR ILE VAL LYS SEQRES 5 D 402 TYR ILE ALA SER HIS ASP ASP ILE ALA LYS ASP PRO LEU SEQRES 6 D 402 PRO THR CYS ASP ALA MET ILE TRP PHE SER ARG ALA LEU SEQRES 7 D 402 ASP ILE GLU ASN ASN ASP VAL LEU VAL LEU GLN GLN ARG SEQRES 8 D 402 LEU TYR GLY LEU VAL LYS LEU LEU GLU PHE ASP TYR SER SEQRES 9 D 402 ASN VAL ILE ALA ILE LEU GLN LYS ILE SER ILE ASN LEU SEQRES 10 D 402 TRP ASN PRO SER THR ASP SER LEU GLN SER LYS HIS PHE SEQRES 11 D 402 LYS THR CYS GLN ASP LYS LEU LYS LEU LEU LEU ASP PHE SEQRES 12 D 402 GLN TRP LYS PHE ASN THR ASN VAL SER PHE GLU ASP ARG SEQRES 13 D 402 THR THR VAL SER LEU LYS ASP LEU GLN CYS ILE LEU ASP SEQRES 14 D 402 ASP GLU ASN GLY LYS CYS GLY LEU ALA HIS SER SER LYS SEQRES 15 D 402 PRO ASN PHE VAL LEU VAL PRO ASN PHE GLN SER PRO PHE SEQRES 16 D 402 THR CYS PRO ILE PHE THR MET ALA VAL TYR TYR TYR LEU SEQRES 17 D 402 ARG PHE HIS GLY VAL LYS LYS TYR TYR LYS GLY ASP GLY SEQRES 18 D 402 TYR GLN ILE LEU SER GLN LEU GLU HIS ILE PRO ILE ILE SEQRES 19 D 402 ARG GLY LYS SER LEU ASP GLN TYR PRO ARG GLU LEU THR SEQRES 20 D 402 LEU GLY ASN TRP TYR PRO THR ILE PHE LYS TYR CYS GLN SEQRES 21 D 402 LEU PRO TYR THR LYS LYS HIS TRP PHE GLN VAL ASN GLN SEQRES 22 D 402 GLU TRP PRO GLN PHE PRO ASP PHE SER ASP SER SER GLU SEQRES 23 D 402 ASN THR SER THR LEU ALA GLU SER ASP SER GLU ASN THR SEQRES 24 D 402 ILE GLY ILE PRO ASP PHE TYR ILE GLU LYS MET ASN ARG SEQRES 25 D 402 THR LYS LEU GLN PRO CYS PRO GLN VAL HIS VAL HIS LEU SEQRES 26 D 402 PHE PRO THR ASP LEU PRO PRO ASP ILE GLN ALA VAL PHE SEQRES 27 D 402 ASP LEU LEU ASN SER VAL LEU VAL THR SER LEU PRO LEU SEQRES 28 D 402 LEU TYR ARG VAL PHE PRO THR HIS ASP ILE PHE LEU ASP SEQRES 29 D 402 PRO SER LEU LYS THR PRO GLN ASN ILE ALA PHE LEU THR SEQRES 30 D 402 GLY THR LEU PRO LEU ASP ILE GLU SER GLN GLU HIS LEU SEQRES 31 D 402 LEU ALA GLN LEU ILE ASP LYS THR GLY THR VAL SER HELIX 1 1 LEU A 4 LYS A 9 5 6 HELIX 2 2 PRO A 12 LYS A 31 1 20 HELIX 3 3 SER A 46 HIS A 57 1 12 HELIX 4 4 HIS A 57 ASP A 63 1 7 HELIX 5 5 PRO A 64 ALA A 77 1 14 HELIX 6 6 GLU A 81 PHE A 101 1 21 HELIX 7 7 VAL A 106 ASN A 119 1 14 HELIX 8 8 THR A 132 ASN A 150 1 19 HELIX 9 9 SER A 152 VAL A 159 1 8 HELIX 10 10 SER A 160 LEU A 164 5 5 HELIX 11 11 SER A 193 THR A 196 5 4 HELIX 12 12 CYS A 197 HIS A 211 1 15 HELIX 13 13 GLN A 223 LEU A 228 1 6 HELIX 14 14 ARG A 244 CYS A 259 1 16 HELIX 15 15 THR A 264 GLN A 270 1 7 HELIX 16 16 PRO A 303 ASN A 311 1 9 HELIX 17 17 PRO A 331 PHE A 356 1 26 HELIX 18 18 HIS A 359 LYS A 368 5 10 HELIX 19 19 THR A 369 THR A 377 1 9 HELIX 20 20 ASP A 383 SER A 386 5 4 HELIX 21 21 GLN A 387 GLN A 393 1 7 HELIX 22 22 LEU D 4 LYS D 9 5 6 HELIX 23 23 PRO D 12 LYS D 31 1 20 HELIX 24 24 LEU D 41 LEU D 45 5 5 HELIX 25 25 SER D 46 HIS D 57 1 12 HELIX 26 26 HIS D 57 ASP D 63 1 7 HELIX 27 27 PRO D 64 ALA D 77 1 14 HELIX 28 28 GLU D 81 PHE D 101 1 21 HELIX 29 29 ASP D 102 ASN D 119 1 18 HELIX 30 30 THR D 132 ASN D 150 1 19 HELIX 31 31 SER D 152 VAL D 159 1 8 HELIX 32 32 SER D 160 LEU D 164 5 5 HELIX 33 33 SER D 193 THR D 196 5 4 HELIX 34 34 CYS D 197 PHE D 210 1 14 HELIX 35 35 GLN D 223 LEU D 228 1 6 HELIX 36 36 ARG D 244 GLN D 260 1 17 HELIX 37 37 THR D 264 GLN D 270 1 7 HELIX 38 38 PRO D 303 ASN D 311 1 9 HELIX 39 39 PRO D 331 PHE D 356 1 26 HELIX 40 40 HIS D 359 LYS D 368 5 10 HELIX 41 41 THR D 369 THR D 377 1 9 HELIX 42 42 ASP D 383 SER D 386 5 4 HELIX 43 43 GLN D 387 GLN D 393 1 7 SHEET 1 A 3 GLN A 165 ASP A 169 0 SHEET 2 A 3 LYS A 174 HIS A 179 -1 O LYS A 174 N ASP A 169 SHEET 3 A 3 PHE A 185 LEU A 187 -1 O LEU A 187 N LEU A 177 SHEET 1 B 2 GLY A 212 VAL A 213 0 SHEET 2 B 2 TYR A 217 LYS A 218 -1 O TYR A 217 N VAL A 213 SHEET 1 C 3 GLN D 165 ASP D 169 0 SHEET 2 C 3 LYS D 174 HIS D 179 -1 O LYS D 174 N ASP D 169 SHEET 3 C 3 PHE D 185 LEU D 187 -1 O PHE D 185 N HIS D 179 CRYST1 93.060 99.651 125.915 90.00 90.00 90.00 P 21 21 21 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 0.010746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007942 0.00000