HEADER TRANSFERASE 26-APR-10 3MPD TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM TITLE 2 ENCEPHALITOZOON CUNICULI, CUBIC FORM, APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDP KINASE, NDPK, NDK; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENCEPHALITOZOON CUNICULI; SOURCE 3 ORGANISM_COMMON: MICROSPORIDIAN PARASITE; SOURCE 4 ORGANISM_TAXID: 6035; SOURCE 5 GENE: ECU06_1530, HM-1:IMSS, NDK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS SSGCID, NIH, NIAID, SBRI, UW, EMERALD BIOSTRUCTURES, ENCEPHALITOZOON KEYWDS 2 CUNICULI, KINASE, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS KEYWDS 3 CENTER FOR INFECTIOUS DISEASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 06-SEP-23 3MPD 1 REMARK SEQADV REVDAT 1 12-MAY-10 3MPD 0 JRNL AUTH A.GARDBERG,T.E.EDWARDS,B.STAKER,SSGCID JRNL TITL CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM JRNL TITL 2 ENCEPHALITOZOON CUNICULI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 27246 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1385 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) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1873 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2316 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.99 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.510 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2402 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3245 ; 1.333 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 306 ; 6.159 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.659 ;23.469 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;14.160 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;12.605 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 361 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1772 ; 0.005 ; 0.021 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): 1482 ; 0.711 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2406 ; 1.287 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 920 ; 2.255 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 833 ; 3.686 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 5 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 27 4 REMARK 3 1 B 1 B 27 4 REMARK 3 2 A 70 A 77 4 REMARK 3 2 B 70 B 77 4 REMARK 3 3 A 80 A 92 4 REMARK 3 3 B 80 B 92 4 REMARK 3 4 A 100 A 106 4 REMARK 3 4 B 100 B 106 4 REMARK 3 5 A 113 A 120 4 REMARK 3 5 B 113 B 120 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 504 ; 0.110 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 504 ; 0.880 ; 2.000 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 1 A 40 REMARK 3 ORIGIN FOR THE GROUP (A): 28.5866 -3.8417 69.9927 REMARK 3 T TENSOR REMARK 3 T11: 0.0767 T22: 0.1366 REMARK 3 T33: 0.0263 T12: 0.0946 REMARK 3 T13: 0.0193 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 1.7389 L22: 1.5891 REMARK 3 L33: 1.3271 L12: 0.4993 REMARK 3 L13: -0.0086 L23: -0.2802 REMARK 3 S TENSOR REMARK 3 S11: 0.0771 S12: 0.0991 S13: 0.0577 REMARK 3 S21: 0.1564 S22: 0.0627 S23: 0.1082 REMARK 3 S31: -0.1968 S32: -0.2926 S33: -0.1398 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 41 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2017 2.4173 85.4560 REMARK 3 T TENSOR REMARK 3 T11: 0.1834 T22: 0.2840 REMARK 3 T33: 0.1378 T12: 0.1499 REMARK 3 T13: 0.0916 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 6.6351 L22: 2.9795 REMARK 3 L33: 12.3703 L12: -0.2426 REMARK 3 L13: 2.6952 L23: -4.7023 REMARK 3 S TENSOR REMARK 3 S11: 0.2332 S12: -0.0823 S13: 0.4197 REMARK 3 S21: 0.1445 S22: 0.0343 S23: 0.2863 REMARK 3 S31: -0.3647 S32: -0.8068 S33: -0.2675 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 63 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6887 -6.7807 73.2864 REMARK 3 T TENSOR REMARK 3 T11: 0.0690 T22: 0.1967 REMARK 3 T33: 0.0602 T12: 0.1018 REMARK 3 T13: 0.0325 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 2.2212 L22: 2.0143 REMARK 3 L33: 2.5235 L12: 1.1796 REMARK 3 L13: 0.0663 L23: 0.3579 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: 0.0932 S13: 0.0112 REMARK 3 S21: 0.1184 S22: 0.0458 S23: 0.2408 REMARK 3 S31: -0.0702 S32: -0.3704 S33: -0.0663 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 91 A 147 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7800 -8.2113 71.1259 REMARK 3 T TENSOR REMARK 3 T11: 0.0417 T22: 0.1497 REMARK 3 T33: 0.0521 T12: 0.0654 REMARK 3 T13: 0.0268 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.3354 L22: 1.4979 REMARK 3 L33: 3.5501 L12: -0.3109 REMARK 3 L13: -0.2901 L23: 0.2997 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.0871 S13: 0.0473 REMARK 3 S21: 0.1520 S22: 0.0532 S23: 0.2337 REMARK 3 S31: -0.2192 S32: -0.6195 S33: -0.0185 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 1 B 40 REMARK 3 ORIGIN FOR THE GROUP (A): 35.4142 2.3396 59.9858 REMARK 3 T TENSOR REMARK 3 T11: 0.1701 T22: 0.1550 REMARK 3 T33: 0.0680 T12: 0.0925 REMARK 3 T13: 0.0003 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 1.7389 L22: 1.5028 REMARK 3 L33: 0.8864 L12: 0.8087 REMARK 3 L13: 0.2440 L23: -0.1705 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: 0.1836 S13: 0.1139 REMARK 3 S21: -0.0857 S22: 0.1184 S23: 0.0050 REMARK 3 S31: -0.2398 S32: -0.2529 S33: -0.1054 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 41 B 62 REMARK 3 ORIGIN FOR THE GROUP (A): 29.1592 9.4822 41.2739 REMARK 3 T TENSOR REMARK 3 T11: 0.1761 T22: 0.2379 REMARK 3 T33: 0.0832 T12: 0.0141 REMARK 3 T13: -0.0928 T23: 0.0786 REMARK 3 L TENSOR REMARK 3 L11: 2.9174 L22: 3.4984 REMARK 3 L33: 11.6095 L12: -1.4644 REMARK 3 L13: -0.9233 L23: 1.3531 REMARK 3 S TENSOR REMARK 3 S11: 0.0704 S12: -0.0717 S13: -0.0114 REMARK 3 S21: 0.0804 S22: 0.1894 S23: 0.0094 REMARK 3 S31: -0.0353 S32: -0.3506 S33: -0.2598 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 63 B 90 REMARK 3 ORIGIN FOR THE GROUP (A): 37.4237 6.3584 55.9230 REMARK 3 T TENSOR REMARK 3 T11: 0.1717 T22: 0.1479 REMARK 3 T33: 0.0698 T12: 0.0810 REMARK 3 T13: 0.0077 T23: 0.0627 REMARK 3 L TENSOR REMARK 3 L11: 2.0557 L22: 3.0157 REMARK 3 L33: 1.7708 L12: 1.2185 REMARK 3 L13: 0.8071 L23: -0.0705 REMARK 3 S TENSOR REMARK 3 S11: -0.0874 S12: 0.2763 S13: 0.2301 REMARK 3 S21: -0.0516 S22: 0.1528 S23: -0.0274 REMARK 3 S31: -0.2905 S32: -0.1298 S33: -0.0654 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 91 B 147 REMARK 3 ORIGIN FOR THE GROUP (A): 38.6767 8.1410 58.5088 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.1013 REMARK 3 T33: 0.0693 T12: 0.0655 REMARK 3 T13: 0.0195 T23: 0.0634 REMARK 3 L TENSOR REMARK 3 L11: 1.2033 L22: 1.3707 REMARK 3 L33: 2.9959 L12: -0.2347 REMARK 3 L13: 0.6965 L23: 0.1305 REMARK 3 S TENSOR REMARK 3 S11: 0.0132 S12: 0.1997 S13: 0.2316 REMARK 3 S21: -0.0564 S22: 0.0114 S23: -0.0564 REMARK 3 S31: -0.5556 S32: -0.2579 S33: -0.0246 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 REMARK 4 REMARK 4 3MPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97650 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27311 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 33.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 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: 1NSQ (DROSOPHILA NDP KINASE) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PACT SCREEN CONDITION F8: 100MM BIS REMARK 280 -TRIS PROPANE PH 6.5, 20% PEG 3350, 200 MM NA2SO4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 290K, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 55.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.66500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.66500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.66500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 55.66500 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 55.66500 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 55.66500 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 55.66500 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 55.66500 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 55.66500 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 55.66500 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 55.66500 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 55.66500 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 55.66500 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 55.66500 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 55.66500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 -1.000000 111.33000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -55.66500 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 55.66500 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 55.66500 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 55.66500 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 111.33000 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 202 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 SER A 0 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 ASP A 134 CG OD1 OD2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 ASP B 133 CG OD1 OD2 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 OH TYR A 147 O HOH A 223 2.08 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 LYS A 111 59.72 -113.64 REMARK 500 ASN A 112 33.01 -97.76 REMARK 500 ILE A 113 -41.95 84.99 REMARK 500 LYS B 111 58.89 -107.28 REMARK 500 ASN B 112 33.61 -93.38 REMARK 500 ILE B 113 -47.45 81.36 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 EDO A 148 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ENCUA.00646.A RELATED DB: TARGETDB DBREF 3MPD A 1 147 UNP Q8SRM7 NDK_ENCCU 1 147 DBREF 3MPD B 1 147 UNP Q8SRM7 NDK_ENCCU 1 147 SEQADV 3MPD GLY A -3 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD PRO A -2 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD GLY A -1 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD SER A 0 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD GLY B -3 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD PRO B -2 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD GLY B -1 UNP Q8SRM7 EXPRESSION TAG SEQADV 3MPD SER B 0 UNP Q8SRM7 EXPRESSION TAG SEQRES 1 A 151 GLY PRO GLY SER MET GLU ARG THR PHE ILE MET ILE LYS SEQRES 2 A 151 PRO ASP ALA ILE LYS ARG ARG LEU ILE SER ARG ILE ILE SEQRES 3 A 151 GLN ARG PHE GLU GLU LYS GLY LEU TYR LEU ALA ALA SER SEQRES 4 A 151 LYS CYS VAL ILE PRO LYS ARG GLU VAL LEU GLU THR HIS SEQRES 5 A 151 TYR SER HIS LEU SER SER MET PRO PHE PHE SER GLU MET SEQRES 6 A 151 VAL GLU ASP MET MET SER GLY MET VAL LEU ALA MET VAL SEQRES 7 A 151 TRP VAL GLY LYS ASP ALA VAL SER ILE GLY ARG LYS LEU SEQRES 8 A 151 ILE GLY GLU THR ASN PRO GLN ALA ALA SER VAL GLY THR SEQRES 9 A 151 ILE ARG GLY ASP TYR GLY VAL SER THR GLY LYS ASN ILE SEQRES 10 A 151 ILE HIS GLY SER ASP CYS VAL GLU ASN ALA GLU LYS GLU SEQRES 11 A 151 ILE LYS LEU TRP ILE GLY ASP ASP VAL GLN PRO VAL SER SEQRES 12 A 151 PHE PHE ASP LYS GLU TRP ILE TYR SEQRES 1 B 151 GLY PRO GLY SER MET GLU ARG THR PHE ILE MET ILE LYS SEQRES 2 B 151 PRO ASP ALA ILE LYS ARG ARG LEU ILE SER ARG ILE ILE SEQRES 3 B 151 GLN ARG PHE GLU GLU LYS GLY LEU TYR LEU ALA ALA SER SEQRES 4 B 151 LYS CYS VAL ILE PRO LYS ARG GLU VAL LEU GLU THR HIS SEQRES 5 B 151 TYR SER HIS LEU SER SER MET PRO PHE PHE SER GLU MET SEQRES 6 B 151 VAL GLU ASP MET MET SER GLY MET VAL LEU ALA MET VAL SEQRES 7 B 151 TRP VAL GLY LYS ASP ALA VAL SER ILE GLY ARG LYS LEU SEQRES 8 B 151 ILE GLY GLU THR ASN PRO GLN ALA ALA SER VAL GLY THR SEQRES 9 B 151 ILE ARG GLY ASP TYR GLY VAL SER THR GLY LYS ASN ILE SEQRES 10 B 151 ILE HIS GLY SER ASP CYS VAL GLU ASN ALA GLU LYS GLU SEQRES 11 B 151 ILE LYS LEU TRP ILE GLY ASP ASP VAL GLN PRO VAL SER SEQRES 12 B 151 PHE PHE ASP LYS GLU TRP ILE TYR HET EDO A 148 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *216(H2 O) HELIX 1 1 LYS A 9 ARG A 15 1 7 HELIX 2 2 LEU A 17 GLY A 29 1 13 HELIX 3 3 LYS A 41 TYR A 49 1 9 HELIX 4 4 SER A 50 SER A 53 5 4 HELIX 5 5 PHE A 57 MET A 66 1 10 HELIX 6 6 ASP A 79 GLY A 89 1 11 HELIX 7 7 THR A 100 GLY A 106 1 7 HELIX 8 8 CYS A 119 ILE A 131 1 13 HELIX 9 9 ASP A 142 TYR A 147 1 6 HELIX 10 10 LYS B 9 ARG B 15 1 7 HELIX 11 11 LEU B 17 GLY B 29 1 13 HELIX 12 12 LYS B 41 TYR B 49 1 9 HELIX 13 13 SER B 50 SER B 53 5 4 HELIX 14 14 PHE B 57 MET B 66 1 10 HELIX 15 15 ASP B 79 GLY B 89 1 11 HELIX 16 16 THR B 100 GLY B 106 1 7 HELIX 17 17 CYS B 119 ILE B 131 1 13 HELIX 18 18 ASP B 142 TYR B 147 1 6 SHEET 1 A 4 TYR A 31 VAL A 38 0 SHEET 2 A 4 VAL A 70 VAL A 76 -1 O VAL A 76 N TYR A 31 SHEET 3 A 4 ARG A 3 ILE A 8 -1 N ILE A 6 O MET A 73 SHEET 4 A 4 ILE A 114 GLY A 116 -1 O HIS A 115 N MET A 7 SHEET 1 B 4 TYR B 31 VAL B 38 0 SHEET 2 B 4 VAL B 70 VAL B 76 -1 O ALA B 72 N LYS B 36 SHEET 3 B 4 ARG B 3 ILE B 8 -1 N THR B 4 O TRP B 75 SHEET 4 B 4 ILE B 114 GLY B 116 -1 O HIS B 115 N MET B 7 SITE 1 AC1 5 PHE A 141 ASP A 142 LYS A 143 GLU A 144 SITE 2 AC1 5 HOH A 243 CRYST1 111.330 111.330 111.330 90.00 90.00 90.00 P 21 3 24 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 0.008982 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008982 0.00000