HEADER HYDROLASE 04-OCT-10 3AON TITLE CRYSTAL STRUCTURE OF THE CENTRAL AXIS (NTPD-NTPG) IN THE CATALYTIC TITLE 2 PORTION OF ENTEROCOCCUS HIRAE V-TYPE SODIUM ATPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: V-TYPE SODIUM ATPASE SUBUNIT D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NA(+)-TRANSLOCATING ATPASE SUBUNIT D, V-TYPE SODIUM PUMP COMPND 5 SUBUNIT D; COMPND 6 EC: 3.6.3.14; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: V-TYPE SODIUM ATPASE SUBUNIT G; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: NA(+)-TRANSLOCATING ATPASE SUBUNIT G, V-TYPE SODIUM PUMP COMPND 12 SUBUNIT G; COMPND 13 EC: 3.6.3.14; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS HIRAE; SOURCE 3 ORGANISM_TAXID: 1354; SOURCE 4 GENE: NTPD; SOURCE 5 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ENTEROCOCCUS HIRAE; SOURCE 8 ORGANISM_TAXID: 1354; SOURCE 9 GENE: NTPG, NTPQ; SOURCE 10 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS KEYWDS V-ATPASE, ENTEROCOCCUS, COILED-COIL, ALPHA/BETA FOLD, HYDROLASE, KEYWDS 2 NA(+)-ATPASE, NTPA3-NTPB3, NTPC, CENTRAL AXIS EXPDTA X-RAY DIFFRACTION AUTHOR S.SAIJO,S.ARAI,K.M.M.HOSSAIN,I.YAMATO,Y.KAKINUMA,Y.ISHIZUKA-KATSURA, AUTHOR 2 T.TERADA,M.SHIROUZU,S.YOKOYAMA,S.IWATA,T.MURATA REVDAT 2 28-DEC-11 3AON 1 JRNL REVDAT 1 05-OCT-11 3AON 0 JRNL AUTH S.SAIJO,S.ARAI,K.M.M.HOSSAIN,I.YAMATO,K.SUZUKI,Y.KAKINUMA, JRNL AUTH 2 Y.ISHIZUKA-KATSURA,N.OHSAWA,T.TERADA,M.SHIROUZU,S.YOKOYAMA, JRNL AUTH 3 S.IWATA,T.MURATA JRNL TITL CRYSTAL STRUCTURE OF THE CENTRAL AXIS DF COMPLEX OF THE JRNL TITL 2 PROKARYOTIC V-ATPASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 19955 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22114184 JRNL DOI 10.1073/PNAS.1108810108 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 31.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 21696 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1085 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) : 1503 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -1.54000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.30000 REMARK 3 B23 (A**2) : 0.00000 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): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.876 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2332 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3149 ; 1.276 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 289 ; 5.019 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;37.267 ;25.619 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;17.468 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.411 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 373 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1698 ; 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): 1447 ; 0.678 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2351 ; 1.306 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 885 ; 2.009 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 797 ; 3.399 ; 4.500 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 : 9 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 7 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8338 -32.6014 23.1548 REMARK 3 T TENSOR REMARK 3 T11: 0.3152 T22: 0.3278 REMARK 3 T33: 0.2926 T12: -0.0326 REMARK 3 T13: -0.0741 T23: 0.1225 REMARK 3 L TENSOR REMARK 3 L11: 2.1400 L22: 1.9618 REMARK 3 L33: 4.8242 L12: -1.7672 REMARK 3 L13: -3.1310 L23: 2.8455 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: -0.0307 S13: -0.0723 REMARK 3 S21: 0.1435 S22: -0.1048 S23: -0.0194 REMARK 3 S31: 0.0793 S32: 0.1119 S33: 0.2014 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 44 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): -9.6583 -1.0416 59.2585 REMARK 3 T TENSOR REMARK 3 T11: 0.1773 T22: 0.3390 REMARK 3 T33: 0.2887 T12: -0.0100 REMARK 3 T13: 0.0892 T23: -0.0853 REMARK 3 L TENSOR REMARK 3 L11: 0.6019 L22: 1.9910 REMARK 3 L33: 2.8555 L12: 0.0317 REMARK 3 L13: 1.1908 L23: 0.9161 REMARK 3 S TENSOR REMARK 3 S11: -0.1423 S12: -0.1205 S13: 0.0813 REMARK 3 S21: 0.2453 S22: -0.0930 S23: 0.2903 REMARK 3 S31: -0.0466 S32: -0.3484 S33: 0.2352 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 86 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1259 -16.7440 47.1255 REMARK 3 T TENSOR REMARK 3 T11: 0.3172 T22: 0.2439 REMARK 3 T33: 0.2722 T12: 0.0305 REMARK 3 T13: -0.0387 T23: -0.0359 REMARK 3 L TENSOR REMARK 3 L11: 0.0540 L22: 7.9773 REMARK 3 L33: 8.3614 L12: 0.0159 REMARK 3 L13: 0.0462 L23: 8.0321 REMARK 3 S TENSOR REMARK 3 S11: 0.1452 S12: -0.0019 S13: 0.0017 REMARK 3 S21: 0.0559 S22: 0.0964 S23: -0.2318 REMARK 3 S31: 0.0984 S32: 0.1075 S33: -0.2416 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 107 A 122 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8031 -7.8584 67.5634 REMARK 3 T TENSOR REMARK 3 T11: 0.5116 T22: 0.2212 REMARK 3 T33: 0.1974 T12: -0.0914 REMARK 3 T13: -0.0129 T23: -0.0731 REMARK 3 L TENSOR REMARK 3 L11: 4.9913 L22: 3.9215 REMARK 3 L33: 1.5091 L12: 0.0720 REMARK 3 L13: 0.7035 L23: 2.3393 REMARK 3 S TENSOR REMARK 3 S11: 0.4351 S12: -0.0198 S13: -0.4459 REMARK 3 S21: 0.4802 S22: -0.4335 S23: -0.1100 REMARK 3 S31: 0.3707 S32: -0.3596 S33: -0.0016 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 : A 123 A 178 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6690 -14.5020 42.3793 REMARK 3 T TENSOR REMARK 3 T11: 0.2519 T22: 0.2889 REMARK 3 T33: 0.2635 T12: -0.0300 REMARK 3 T13: 0.0289 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.1459 L22: 2.0579 REMARK 3 L33: 6.4556 L12: -0.0588 REMARK 3 L13: 0.2404 L23: 3.3587 REMARK 3 S TENSOR REMARK 3 S11: 0.0599 S12: -0.0342 S13: 0.0279 REMARK 3 S21: -0.0415 S22: -0.0426 S23: 0.0741 REMARK 3 S31: 0.0359 S32: -0.0670 S33: -0.0173 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 : A 179 A 194 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2918 -38.4763 -0.3754 REMARK 3 T TENSOR REMARK 3 T11: 0.3041 T22: 0.5756 REMARK 3 T33: 0.0602 T12: 0.3919 REMARK 3 T13: 0.0202 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 6.2624 L22: 10.5414 REMARK 3 L33: 13.8681 L12: -5.9525 REMARK 3 L13: -9.3187 L23: 8.7958 REMARK 3 S TENSOR REMARK 3 S11: 0.3757 S12: 0.3683 S13: -0.3921 REMARK 3 S21: -0.5849 S22: -0.9823 S23: 0.2095 REMARK 3 S31: -0.5263 S32: -0.5388 S33: 0.6066 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 1 B 42 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2581 2.8881 49.2394 REMARK 3 T TENSOR REMARK 3 T11: 0.2246 T22: 0.2411 REMARK 3 T33: 0.2933 T12: -0.0077 REMARK 3 T13: 0.0107 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.6580 L22: 2.1028 REMARK 3 L33: 1.9217 L12: 0.3099 REMARK 3 L13: 1.0600 L23: 1.0070 REMARK 3 S TENSOR REMARK 3 S11: -0.1426 S12: -0.0008 S13: 0.2285 REMARK 3 S21: -0.0111 S22: -0.0981 S23: -0.1288 REMARK 3 S31: -0.1887 S32: 0.0886 S33: 0.2407 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 43 B 86 REMARK 3 ORIGIN FOR THE GROUP (A): -5.3536 -2.3616 42.9431 REMARK 3 T TENSOR REMARK 3 T11: 0.1908 T22: 0.3001 REMARK 3 T33: 0.2845 T12: 0.0089 REMARK 3 T13: 0.0247 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.3737 L22: 1.6386 REMARK 3 L33: 1.5397 L12: -0.2526 REMARK 3 L13: 0.2061 L23: 0.8523 REMARK 3 S TENSOR REMARK 3 S11: -0.0504 S12: 0.0295 S13: 0.0866 REMARK 3 S21: -0.0993 S22: -0.1324 S23: 0.0695 REMARK 3 S31: -0.0709 S32: -0.0303 S33: 0.1828 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 87 B 101 REMARK 3 ORIGIN FOR THE GROUP (A): -14.3935 -13.7868 34.5758 REMARK 3 T TENSOR REMARK 3 T11: 0.3032 T22: 0.2833 REMARK 3 T33: 0.2534 T12: -0.0521 REMARK 3 T13: -0.0213 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 3.1590 L22: 8.5173 REMARK 3 L33: 11.4201 L12: 1.6521 REMARK 3 L13: 1.6112 L23: 9.8451 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: -0.1246 S13: 0.5062 REMARK 3 S21: -0.0898 S22: -0.3608 S23: 0.3945 REMARK 3 S31: -0.0477 S32: -0.4437 S33: 0.4186 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 3AON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB029507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9794, 1.0000 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 34.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 0.2 M SODIUM NITRATE, REMARK 280 0.1M MES-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.89350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.21650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.89350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.21650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 295 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 239 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 -6 REMARK 465 SER A -5 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 MSE A 1 REMARK 465 ARG A 2 REMARK 465 LEU A 3 REMARK 465 ASN A 4 REMARK 465 VAL A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 195 REMARK 465 GLU A 196 REMARK 465 VAL A 197 REMARK 465 THR A 198 REMARK 465 ARG A 199 REMARK 465 LEU A 200 REMARK 465 ILE A 201 REMARK 465 LYS A 202 REMARK 465 VAL A 203 REMARK 465 LYS A 204 REMARK 465 ASN A 205 REMARK 465 MSE A 206 REMARK 465 GLY A 207 REMARK 465 THR A 208 REMARK 465 GLU A 209 REMARK 465 GLU A 210 REMARK 465 ILE B 102 REMARK 465 LEU B 103 REMARK 465 SER B 104 REMARK 465 GLY B 105 REMARK 465 PRO B 106 REMARK 465 SER B 107 REMARK 465 SER B 108 REMARK 465 GLY B 109 REMARK 465 GLU B 110 REMARK 465 ASN B 111 REMARK 465 LEU B 112 REMARK 465 TYR B 113 REMARK 465 PHE B 114 REMARK 465 GLN B 115 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 ARG A 9 NE CZ NH1 NH2 REMARK 470 LYS A 46 CD CE NZ REMARK 470 LYS A 101 CE NZ REMARK 470 GLU A 115 CG CD OE1 OE2 REMARK 470 LEU A 123 CG CD1 CD2 REMARK 470 HIS A 124 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 142 CE NZ REMARK 470 LYS A 188 CD CE NZ REMARK 470 ARG A 194 CD NE CZ NH1 NH2 REMARK 470 LYS B 4 CD CE NZ REMARK 470 LYS B 11 CE NZ REMARK 470 LYS B 35 CE NZ REMARK 470 GLU B 39 CD OE1 OE2 REMARK 470 LYS B 42 CE NZ 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 ND2 ASN A 87 O HOH A 263 2.14 REMARK 500 OE1 GLN B 68 O HOH B 152 2.16 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 MSE A 98 -122.26 56.29 REMARK 500 MSE A 173 -62.29 -122.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 92 23.5 L L OUTSIDE RANGE 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 261 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH B 145 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH B 148 DISTANCE = 6.47 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 116 REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST AND WILL BE DEPOSITED TO DATABASE. THE N-TERMINAL GSSGSSG ARE REMARK 999 EXPRESSION TAGS. DBREF 3AON A -6 210 PDB 3AON 3AON 1 217 DBREF 3AON B 1 103 UNP P43455 NTPG_ENTHR 1 103 SEQADV 3AON SER B 104 UNP P43455 EXPRESSION TAG SEQADV 3AON GLY B 105 UNP P43455 EXPRESSION TAG SEQADV 3AON PRO B 106 UNP P43455 EXPRESSION TAG SEQADV 3AON SER B 107 UNP P43455 EXPRESSION TAG SEQADV 3AON SER B 108 UNP P43455 EXPRESSION TAG SEQADV 3AON GLY B 109 UNP P43455 EXPRESSION TAG SEQADV 3AON GLU B 110 UNP P43455 EXPRESSION TAG SEQADV 3AON ASN B 111 UNP P43455 EXPRESSION TAG SEQADV 3AON LEU B 112 UNP P43455 EXPRESSION TAG SEQADV 3AON TYR B 113 UNP P43455 EXPRESSION TAG SEQADV 3AON PHE B 114 UNP P43455 EXPRESSION TAG SEQADV 3AON GLN B 115 UNP P43455 EXPRESSION TAG SEQRES 1 A 217 GLY SER SER GLY SER SER GLY MSE ARG LEU ASN VAL ASN SEQRES 2 A 217 PRO THR ARG MSE GLU LEU THR ARG LEU LYS LYS GLN LEU SEQRES 3 A 217 THR THR ALA THR ARG GLY HIS LYS LEU LEU LYS ASP LYS SEQRES 4 A 217 GLN ASP GLU LEU MSE ARG GLN PHE ILE LEU LEU ILE ARG SEQRES 5 A 217 LYS ASN ASN GLU LEU ARG GLN ALA ILE GLU LYS GLU THR SEQRES 6 A 217 GLN THR ALA MSE LYS ASP PHE VAL LEU ALA LYS SER THR SEQRES 7 A 217 VAL GLU GLU ALA PHE ILE ASP GLU LEU LEU ALA LEU PRO SEQRES 8 A 217 ALA GLU ASN VAL SER ILE SER VAL VAL GLU LYS ASN ILE SEQRES 9 A 217 MSE SER VAL LYS VAL PRO LEU MSE ASN PHE GLN TYR ASP SEQRES 10 A 217 GLU THR LEU ASN GLU THR PRO LEU GLU TYR GLY TYR LEU SEQRES 11 A 217 HIS SER ASN ALA GLU LEU ASP ARG SER ILE ASP GLY PHE SEQRES 12 A 217 THR GLN LEU LEU PRO LYS LEU LEU LYS LEU ALA GLU VAL SEQRES 13 A 217 GLU LYS THR CYS GLN LEU MSE ALA GLU GLU ILE GLU LYS SEQRES 14 A 217 THR ARG ARG ARG VAL ASN ALA LEU GLU TYR MSE THR ILE SEQRES 15 A 217 PRO GLN LEU GLU GLU THR ILE TYR TYR ILE LYS MSE LYS SEQRES 16 A 217 LEU GLU GLU ASN GLU ARG ALA GLU VAL THR ARG LEU ILE SEQRES 17 A 217 LYS VAL LYS ASN MSE GLY THR GLU GLU SEQRES 1 B 115 MSE THR TYR LYS ILE GLY VAL VAL GLY ASP LYS ASP SER SEQRES 2 B 115 VAL SER PRO PHE ARG LEU PHE GLY PHE ASP VAL GLN HIS SEQRES 3 B 115 GLY THR THR LYS THR GLU ILE ARG LYS THR ILE ASP GLU SEQRES 4 B 115 MSE ALA LYS ASN GLU TYR GLY VAL ILE TYR ILE THR GLU SEQRES 5 B 115 GLN CYS ALA ASN LEU VAL PRO GLU THR ILE GLU ARG TYR SEQRES 6 B 115 LYS GLY GLN LEU THR PRO ALA ILE ILE LEU ILE PRO SER SEQRES 7 B 115 HIS GLN GLY THR LEU GLY ILE GLY LEU GLU GLU ILE GLN SEQRES 8 B 115 ASN SER VAL GLU LYS ALA VAL GLY GLN ASN ILE LEU SER SEQRES 9 B 115 GLY PRO SER SER GLY GLU ASN LEU TYR PHE GLN MODRES 3AON MSE A 10 MET SELENOMETHIONINE MODRES 3AON MSE A 37 MET SELENOMETHIONINE MODRES 3AON MSE A 62 MET SELENOMETHIONINE MODRES 3AON MSE A 98 MET SELENOMETHIONINE MODRES 3AON MSE A 105 MET SELENOMETHIONINE MODRES 3AON MSE A 156 MET SELENOMETHIONINE MODRES 3AON MSE A 173 MET SELENOMETHIONINE MODRES 3AON MSE A 187 MET SELENOMETHIONINE MODRES 3AON MSE B 1 MET SELENOMETHIONINE MODRES 3AON MSE B 40 MET SELENOMETHIONINE HET MSE A 10 8 HET MSE A 37 8 HET MSE A 62 8 HET MSE A 98 8 HET MSE A 105 8 HET MSE A 156 8 HET MSE A 173 8 HET MSE A 187 13 HET MSE B 1 8 HET MSE B 40 8 HET NO3 B 116 4 HETNAM MSE SELENOMETHIONINE HETNAM NO3 NITRATE ION FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 NO3 N O3 1- FORMUL 4 HOH *152(H2 O) HELIX 1 1 THR A 8 SER A 70 1 63 HELIX 2 2 GLU A 73 ALA A 82 1 10 HELIX 3 3 ASP A 110 ASN A 114 5 5 HELIX 4 4 ASN A 126 MSE A 173 1 48 HELIX 5 5 MSE A 173 ARG A 194 1 22 HELIX 6 6 ASP B 10 SER B 15 1 6 HELIX 7 7 PRO B 16 GLY B 21 5 6 HELIX 8 8 THR B 29 ASN B 43 1 15 HELIX 9 9 GLU B 52 ASN B 56 1 5 HELIX 10 10 VAL B 58 GLY B 67 1 10 HELIX 11 11 GLY B 84 VAL B 98 1 15 SHEET 1 A 4 VAL A 100 GLN A 108 0 SHEET 2 A 4 SER A 89 ILE A 97 -1 N SER A 89 O GLN A 108 SHEET 3 A 4 THR B 2 VAL B 8 -1 O TYR B 3 N ILE A 90 SHEET 4 A 4 ASP B 23 GLN B 25 1 O GLN B 25 N VAL B 7 SHEET 1 B 5 VAL A 100 GLN A 108 0 SHEET 2 B 5 SER A 89 ILE A 97 -1 N SER A 89 O GLN A 108 SHEET 3 B 5 THR B 2 VAL B 8 -1 O TYR B 3 N ILE A 90 SHEET 4 B 5 TYR B 45 THR B 51 1 O TYR B 49 N VAL B 8 SHEET 5 B 5 ALA B 72 ILE B 76 1 O ALA B 72 N ILE B 48 LINK C ARG A 9 N MSE A 10 1555 1555 1.33 LINK C MSE A 10 N GLU A 11 1555 1555 1.33 LINK C LEU A 36 N MSE A 37 1555 1555 1.33 LINK C MSE A 37 N ARG A 38 1555 1555 1.33 LINK C ALA A 61 N MSE A 62 1555 1555 1.33 LINK C MSE A 62 N LYS A 63 1555 1555 1.33 LINK C ILE A 97 N MSE A 98 1555 1555 1.34 LINK C MSE A 98 N SER A 99 1555 1555 1.33 LINK C LEU A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N ASN A 106 1555 1555 1.33 LINK C LEU A 155 N MSE A 156 1555 1555 1.33 LINK C MSE A 156 N ALA A 157 1555 1555 1.33 LINK C TYR A 172 N MSE A 173 1555 1555 1.33 LINK C MSE A 173 N THR A 174 1555 1555 1.34 LINK C LYS A 186 N MSE A 187 1555 1555 1.34 LINK C MSE A 187 N LYS A 188 1555 1555 1.34 LINK C MSE B 1 N THR B 2 1555 1555 1.34 LINK C GLU B 39 N MSE B 40 1555 1555 1.33 LINK C MSE B 40 N ALA B 41 1555 1555 1.33 CISPEP 1 THR B 70 PRO B 71 0 1.54 SITE 1 AC1 3 GLY B 81 THR B 82 LEU B 83 CRYST1 105.787 68.433 51.153 90.00 114.99 90.00 C 1 2 1 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 0.009453 0.000000 0.004407 0.00000 SCALE2 0.000000 0.014613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021569 0.00000