HEADER TRANSFERASE 09-APR-12 4EK2 TITLE THE STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE (NDK) FROM BURKHOLDERIA TITLE 2 THAILANDENSIS BOUND TO DEOXYADENOSINE MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA THAILANDENSIS; SOURCE 3 ORGANISM_TAXID: 271848; SOURCE 4 STRAIN: E264 / ATCC 700388 / DSM 13276 / CIP 106301; SOURCE 5 GENE: NDK, BTH_I2231; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID, KEYWDS 2 DAMP, NIAID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 29-MAY-24 4EK2 1 REMARK HET SITE ATOM REVDAT 3 13-SEP-23 4EK2 1 REMARK SEQADV REVDAT 2 30-OCT-13 4EK2 1 JRNL REVDAT 1 09-MAY-12 4EK2 0 JRNL AUTH L.BAUGH,L.A.GALLAGHER,R.PATRAPUVICH,M.C.CLIFTON, JRNL AUTH 2 A.S.GARDBERG,T.E.EDWARDS,B.ARMOUR,D.W.BEGLEY,S.H.DIETERICH, JRNL AUTH 3 D.M.DRANOW,J.ABENDROTH,J.W.FAIRMAN,D.FOX,B.L.STAKER,I.PHAN, JRNL AUTH 4 A.GILLESPIE,R.CHOI,S.NAKAZAWA-HEWITT,M.T.NGUYEN,A.NAPULI, JRNL AUTH 5 L.BARRETT,G.W.BUCHKO,R.STACY,P.J.MYLER,L.J.STEWART,C.MANOIL, JRNL AUTH 6 W.C.VAN VOORHIS JRNL TITL COMBINING FUNCTIONAL AND STRUCTURAL GENOMICS TO SAMPLE THE JRNL TITL 2 ESSENTIAL BURKHOLDERIA STRUCTOME. JRNL REF PLOS ONE V. 8 53851 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23382856 JRNL DOI 10.1371/JOURNAL.PONE.0053851 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 25383 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1295 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1504 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : 0.49000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.791 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2285 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1546 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3099 ; 1.332 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3756 ; 0.923 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 5.729 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;32.722 ;23.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;14.022 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;18.641 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 346 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2584 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 484 ; 0.001 ; 0.020 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): 1431 ; 0.615 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 571 ; 0.159 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 1.103 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 854 ; 1.885 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 799 ; 3.149 ; 4.500 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 : 8 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 0 A 45 REMARK 3 ORIGIN FOR THE GROUP (A): -16.2148 24.2287 -5.2175 REMARK 3 T TENSOR REMARK 3 T11: 0.0318 T22: 0.0415 REMARK 3 T33: 0.0299 T12: -0.0012 REMARK 3 T13: 0.0100 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 1.6470 L22: 0.6818 REMARK 3 L33: 0.6444 L12: 0.1689 REMARK 3 L13: 0.0786 L23: -0.2678 REMARK 3 S TENSOR REMARK 3 S11: -0.0367 S12: 0.1394 S13: -0.1117 REMARK 3 S21: -0.0646 S22: 0.0398 S23: 0.0290 REMARK 3 S31: 0.0174 S32: -0.0495 S33: -0.0031 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 : A 46 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5639 7.2396 -1.3805 REMARK 3 T TENSOR REMARK 3 T11: 0.1676 T22: 0.0307 REMARK 3 T33: 0.2802 T12: 0.0011 REMARK 3 T13: 0.0648 T23: -0.0803 REMARK 3 L TENSOR REMARK 3 L11: 5.6279 L22: 3.2572 REMARK 3 L33: 2.9684 L12: 0.5362 REMARK 3 L13: 1.2334 L23: -0.4976 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: 0.4131 S13: -0.8634 REMARK 3 S21: -0.4572 S22: -0.0452 S23: -0.2445 REMARK 3 S31: 0.4023 S32: 0.1392 S33: 0.0644 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 : A 71 A 94 REMARK 3 ORIGIN FOR THE GROUP (A): -18.3990 21.2666 -11.1139 REMARK 3 T TENSOR REMARK 3 T11: 0.0679 T22: 0.0696 REMARK 3 T33: 0.0375 T12: -0.0041 REMARK 3 T13: 0.0091 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 3.5571 L22: 1.0086 REMARK 3 L33: 1.9352 L12: 0.0698 REMARK 3 L13: 0.8701 L23: 0.0098 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.3190 S13: -0.2364 REMARK 3 S21: -0.1861 S22: 0.0323 S23: -0.0039 REMARK 3 S31: 0.1496 S32: -0.0950 S33: -0.0654 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 : A 95 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4796 18.6421 -7.4939 REMARK 3 T TENSOR REMARK 3 T11: 0.0342 T22: 0.0623 REMARK 3 T33: 0.0393 T12: 0.0028 REMARK 3 T13: 0.0002 T23: -0.0406 REMARK 3 L TENSOR REMARK 3 L11: 1.8692 L22: 1.0748 REMARK 3 L33: 0.9838 L12: 0.4498 REMARK 3 L13: -0.1262 L23: 0.1222 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: 0.2931 S13: -0.2610 REMARK 3 S21: -0.0351 S22: 0.0712 S23: -0.1083 REMARK 3 S31: 0.0928 S32: -0.0434 S33: -0.0282 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 : B 2 B 48 REMARK 3 ORIGIN FOR THE GROUP (A): -16.4563 36.4748 3.3840 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0212 REMARK 3 T33: 0.0358 T12: 0.0053 REMARK 3 T13: 0.0103 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.0627 L22: 0.6971 REMARK 3 L33: 0.9478 L12: 0.0199 REMARK 3 L13: -0.1697 L23: -0.0082 REMARK 3 S TENSOR REMARK 3 S11: 0.0200 S12: -0.0118 S13: 0.0411 REMARK 3 S21: 0.0395 S22: 0.0284 S23: 0.0359 REMARK 3 S31: -0.0820 S32: -0.0277 S33: -0.0485 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 : B 49 B 67 REMARK 3 ORIGIN FOR THE GROUP (A): -26.9232 47.7022 12.6425 REMARK 3 T TENSOR REMARK 3 T11: 0.2449 T22: 0.0908 REMARK 3 T33: 0.0393 T12: 0.0213 REMARK 3 T13: 0.0949 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.5888 L22: 7.5986 REMARK 3 L33: 5.4398 L12: 0.4269 REMARK 3 L13: 1.7394 L23: 1.8586 REMARK 3 S TENSOR REMARK 3 S11: 0.2047 S12: -0.2293 S13: 0.1411 REMARK 3 S21: -0.0817 S22: -0.1107 S23: 0.2349 REMARK 3 S31: -0.5989 S32: -0.2252 S33: -0.0940 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 68 B 93 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4724 41.0119 6.0962 REMARK 3 T TENSOR REMARK 3 T11: 0.0690 T22: 0.0298 REMARK 3 T33: 0.0311 T12: 0.0013 REMARK 3 T13: 0.0231 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 3.0983 L22: 1.4745 REMARK 3 L33: 0.3274 L12: -0.5632 REMARK 3 L13: 0.3145 L23: -0.1361 REMARK 3 S TENSOR REMARK 3 S11: 0.0586 S12: -0.1022 S13: 0.0724 REMARK 3 S21: 0.0805 S22: 0.0142 S23: -0.1152 REMARK 3 S31: -0.1102 S32: 0.0036 S33: -0.0728 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 94 B 141 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8641 40.8520 7.1162 REMARK 3 T TENSOR REMARK 3 T11: 0.0334 T22: 0.0195 REMARK 3 T33: 0.0536 T12: -0.0051 REMARK 3 T13: 0.0275 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.7919 L22: 1.4335 REMARK 3 L33: 1.3596 L12: -0.0441 REMARK 3 L13: -0.2357 L23: -0.2720 REMARK 3 S TENSOR REMARK 3 S11: 0.0829 S12: -0.0229 S13: 0.1214 REMARK 3 S21: 0.0626 S22: -0.0161 S23: 0.0443 REMARK 3 S31: -0.1788 S32: -0.0079 S33: -0.0668 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: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4EK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25415 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.553 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.950 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 4DUT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BUTHA.00438.A.A1 PS01186 AT 42.64 REMARK 280 MG/ML IN 1.5 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 7.0, REMARK 280 10 MM DAMP, CRYOPROTECTANT: 15% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.21500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.60750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.82250 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.21500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.82250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.60750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 389 LIES ON A SPECIAL POSITION. 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 -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 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 0 OG REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LEU A 84 CG CD1 CD2 REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 LYS B 96 CG CD CE NZ REMARK 470 LYS B 100 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 ALA A 115 -42.12 74.30 REMARK 500 ALA B 115 -44.06 76.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D5M A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DUT RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO DEOXYADENOSINE MONOPHOSPHATE REMARK 900 RELATED ID: SSGCID-BUTHA.00438.A RELATED DB: TARGETTRACK DBREF 4EK2 A 1 141 UNP Q2SWE7 NDK_BURTA 1 141 DBREF 4EK2 B 1 141 UNP Q2SWE7 NDK_BURTA 1 141 SEQADV 4EK2 GLY A -3 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 PRO A -2 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 GLY A -1 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 SER A 0 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 GLY B -3 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 PRO B -2 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 GLY B -1 UNP Q2SWE7 EXPRESSION TAG SEQADV 4EK2 SER B 0 UNP Q2SWE7 EXPRESSION TAG SEQRES 1 A 145 GLY PRO GLY SER MET ALA LEU GLU ARG THR LEU SER ILE SEQRES 2 A 145 ILE LYS PRO ASP ALA VAL ALA LYS ASN VAL ILE GLY GLN SEQRES 3 A 145 ILE TYR SER ARG PHE GLU ASN ALA GLY LEU LYS ILE VAL SEQRES 4 A 145 ALA ALA ARG MET ALA HIS LEU SER ARG ALA ASP ALA GLU SEQRES 5 A 145 LYS PHE TYR ALA VAL HIS ALA GLU ARG PRO PHE PHE LYS SEQRES 6 A 145 ASP LEU VAL GLU PHE MET ILE SER GLY PRO VAL MET ILE SEQRES 7 A 145 GLN VAL LEU GLU GLY GLU ASP ALA ILE LEU LYS ASN ARG SEQRES 8 A 145 ASP LEU MET GLY ALA THR ASP PRO LYS LYS ALA GLU LYS SEQRES 9 A 145 GLY THR ILE ARG ALA ASP PHE ALA ASP SER ILE ASP ALA SEQRES 10 A 145 ASN ALA VAL HIS GLY SER ASP ALA PRO GLU THR ALA ARG SEQRES 11 A 145 VAL GLU ILE ALA PHE PHE PHE PRO GLU MET ASN VAL TYR SEQRES 12 A 145 SER ARG SEQRES 1 B 145 GLY PRO GLY SER MET ALA LEU GLU ARG THR LEU SER ILE SEQRES 2 B 145 ILE LYS PRO ASP ALA VAL ALA LYS ASN VAL ILE GLY GLN SEQRES 3 B 145 ILE TYR SER ARG PHE GLU ASN ALA GLY LEU LYS ILE VAL SEQRES 4 B 145 ALA ALA ARG MET ALA HIS LEU SER ARG ALA ASP ALA GLU SEQRES 5 B 145 LYS PHE TYR ALA VAL HIS ALA GLU ARG PRO PHE PHE LYS SEQRES 6 B 145 ASP LEU VAL GLU PHE MET ILE SER GLY PRO VAL MET ILE SEQRES 7 B 145 GLN VAL LEU GLU GLY GLU ASP ALA ILE LEU LYS ASN ARG SEQRES 8 B 145 ASP LEU MET GLY ALA THR ASP PRO LYS LYS ALA GLU LYS SEQRES 9 B 145 GLY THR ILE ARG ALA ASP PHE ALA ASP SER ILE ASP ALA SEQRES 10 B 145 ASN ALA VAL HIS GLY SER ASP ALA PRO GLU THR ALA ARG SEQRES 11 B 145 VAL GLU ILE ALA PHE PHE PHE PRO GLU MET ASN VAL TYR SEQRES 12 B 145 SER ARG HET CL A 201 1 HET DMS A 202 4 HET D5M A 203 22 HET CL B 201 1 HET EDO B 202 4 HET DMS B 203 4 HETNAM CL CHLORIDE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CL 2(CL 1-) FORMUL 4 DMS 2(C2 H6 O S) FORMUL 5 D5M C10 H14 N5 O6 P FORMUL 7 EDO C2 H6 O2 FORMUL 9 HOH *275(H2 O) HELIX 1 1 LYS A 11 LYS A 17 1 7 HELIX 2 2 VAL A 19 ALA A 30 1 12 HELIX 3 3 SER A 43 TYR A 51 1 9 HELIX 4 4 ALA A 52 ALA A 55 5 4 HELIX 5 5 PHE A 59 ILE A 68 1 10 HELIX 6 6 ASP A 81 GLY A 91 1 11 HELIX 7 7 THR A 102 ALA A 108 1 7 HELIX 8 8 ALA A 121 PHE A 133 1 13 HELIX 9 9 PRO A 134 VAL A 138 5 5 HELIX 10 10 LYS B 11 LYS B 17 1 7 HELIX 11 11 VAL B 19 ALA B 30 1 12 HELIX 12 12 SER B 43 TYR B 51 1 9 HELIX 13 13 ALA B 52 ALA B 55 5 4 HELIX 14 14 PHE B 59 ILE B 68 1 10 HELIX 15 15 ASP B 81 GLY B 91 1 11 HELIX 16 16 THR B 102 ALA B 108 1 7 HELIX 17 17 ALA B 121 PHE B 133 1 13 HELIX 18 18 PRO B 134 VAL B 138 5 5 SHEET 1 A 4 LYS A 33 ALA A 40 0 SHEET 2 A 4 VAL A 72 GLU A 80 -1 O VAL A 72 N ALA A 40 SHEET 3 A 4 LEU A 3 ILE A 10 -1 N ILE A 10 O MET A 73 SHEET 4 A 4 VAL A 116 GLY A 118 -1 O HIS A 117 N ILE A 9 SHEET 1 B 4 LYS B 33 ALA B 40 0 SHEET 2 B 4 VAL B 72 GLU B 78 -1 O ILE B 74 N ARG B 38 SHEET 3 B 4 ARG B 5 ILE B 10 -1 N ILE B 10 O MET B 73 SHEET 4 B 4 VAL B 116 GLY B 118 -1 O HIS B 117 N ILE B 9 SITE 1 AC1 3 LYS A 11 TYR A 51 HIS A 117 SITE 1 AC2 8 GLU A 4 ARG A 5 PRO A 122 ALA A 125 SITE 2 AC2 8 ARG A 126 ILE A 129 D5M A 203 HOH A 430 SITE 1 AC3 11 ALA A 2 LEU A 3 DMS A 202 HOH A 349 SITE 2 AC3 11 HOH A 429 HOH A 430 PHE B 59 LEU B 63 SITE 3 AC3 11 THR B 93 ASP B 112 HOH B 399 SITE 1 AC4 3 LYS B 11 TYR B 51 HIS B 117 SITE 1 AC5 5 PHE B 50 TYR B 51 VAL B 53 HIS B 54 SITE 2 AC5 5 GLU B 128 SITE 1 AC6 4 GLU B 4 ARG B 5 PRO B 122 ARG B 126 CRYST1 90.680 90.680 90.430 90.00 90.00 90.00 P 41 2 2 16 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 0.011028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011058 0.00000