HEADER METAL BINDING PROTEIN 04-JUN-14 4TNN TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI PROTEIN YODA IN COMPLEX WITH NI TITLE 2 - ARTIFACT OF PURIFICATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL-BINDING LIPOCALIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100; SOURCE 3 ORGANISM_TAXID: 1403831; SOURCE 4 GENE: YODA, BN896_1774; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSGC-HIS KEYWDS YODA, PURIFICATION ARTIFACT, METAL-BINDING LIPOCALIN, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.A.GASIOROWSKA,M.T.CYMBOROWSKI,K.B.HANDING,I.G.SHABALIN, AUTHOR 2 E.ZASADZINSKA,E.NIEDZIALKOWSKA,P.J.POREBSKI,W.MINOR REVDAT 8 27-SEP-23 4TNN 1 REMARK REVDAT 7 13-APR-22 4TNN 1 AUTHOR JRNL LINK REVDAT 6 25-DEC-19 4TNN 1 REMARK REVDAT 5 06-SEP-17 4TNN 1 REMARK REVDAT 4 19-APR-17 4TNN 1 JRNL REVDAT 3 26-AUG-15 4TNN 1 REMARK REVDAT 2 24-SEP-14 4TNN 1 REMARK REVDAT 1 25-JUN-14 4TNN 0 JRNL AUTH E.NIEDZIALKOWSKA,O.GASIOROWSKA,K.B.HANDING,K.A.MAJOREK, JRNL AUTH 2 P.J.POREBSKI,I.G.SHABALIN,E.ZASADZINSKA,M.CYMBOROWSKI, JRNL AUTH 3 W.MINOR JRNL TITL PROTEIN PURIFICATION AND CRYSTALLIZATION ARTIFACTS: THE TALE JRNL TITL 2 USUALLY NOT TOLD. JRNL REF PROTEIN SCI. V. 25 720 2016 JRNL REFN ESSN 1469-896X JRNL PMID 26660914 JRNL DOI 10.1002/PRO.2861 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15616 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 782 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.64000 REMARK 3 B12 (A**2) : 0.10000 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): 0.154 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.694 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1620 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1406 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2200 ; 1.500 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3255 ; 0.772 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 194 ; 6.492 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;30.206 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 261 ;14.378 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;15.162 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 226 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1839 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 379 ; 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): 773 ; 1.416 ; 1.902 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 772 ; 1.417 ; 1.903 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 965 ; 2.020 ; 2.844 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 1 A 15 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4490 41.2750 1.8700 REMARK 3 T TENSOR REMARK 3 T11: 0.0877 T22: 0.0510 REMARK 3 T33: 0.0458 T12: 0.0466 REMARK 3 T13: -0.0264 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 1.5255 L22: 1.4804 REMARK 3 L33: 23.5047 L12: 0.9098 REMARK 3 L13: 1.8113 L23: 0.2800 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.1365 S13: -0.0627 REMARK 3 S21: -0.0372 S22: 0.0659 S23: -0.1533 REMARK 3 S31: 1.1492 S32: 0.8591 S33: -0.0682 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 16 A 37 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4700 32.2830 -10.7530 REMARK 3 T TENSOR REMARK 3 T11: 0.0918 T22: 0.2045 REMARK 3 T33: 0.0689 T12: -0.0296 REMARK 3 T13: -0.0380 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.5882 L22: 3.1742 REMARK 3 L33: 3.1417 L12: 0.1608 REMARK 3 L13: -0.0264 L23: -2.1833 REMARK 3 S TENSOR REMARK 3 S11: 0.0954 S12: 0.1222 S13: -0.1470 REMARK 3 S21: 0.0505 S22: -0.1854 S23: -0.2801 REMARK 3 S31: -0.0351 S32: 0.4430 S33: 0.0901 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 38 A 56 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6710 35.1370 4.6300 REMARK 3 T TENSOR REMARK 3 T11: 0.1699 T22: 0.5046 REMARK 3 T33: 0.0861 T12: -0.0694 REMARK 3 T13: 0.0641 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 7.1096 L22: 3.7637 REMARK 3 L33: 1.1932 L12: -4.3353 REMARK 3 L13: 1.7386 L23: -0.1573 REMARK 3 S TENSOR REMARK 3 S11: -0.2051 S12: -1.0985 S13: -0.0825 REMARK 3 S21: 0.3501 S22: 0.3196 S23: -0.0633 REMARK 3 S31: 0.1346 S32: -0.4570 S33: -0.1145 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 57 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): -18.9560 45.2110 -3.9580 REMARK 3 T TENSOR REMARK 3 T11: 0.1391 T22: 0.1614 REMARK 3 T33: 0.1928 T12: -0.0578 REMARK 3 T13: 0.1153 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 5.9810 L22: 16.9259 REMARK 3 L33: 10.3835 L12: -2.6530 REMARK 3 L13: -2.0487 L23: -6.7592 REMARK 3 S TENSOR REMARK 3 S11: 0.6592 S12: 0.0646 S13: 0.6461 REMARK 3 S21: 0.0885 S22: -0.4025 S23: 0.0744 REMARK 3 S31: -0.8632 S32: 0.4851 S33: -0.2567 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 75 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): -8.6660 21.8490 0.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.1226 T22: 0.1743 REMARK 3 T33: 0.1551 T12: -0.0829 REMARK 3 T13: -0.0226 T23: 0.1031 REMARK 3 L TENSOR REMARK 3 L11: 6.6422 L22: 4.8967 REMARK 3 L33: 2.3196 L12: -4.1173 REMARK 3 L13: 0.0338 L23: 0.4753 REMARK 3 S TENSOR REMARK 3 S11: 0.1529 S12: -0.2848 S13: -0.6891 REMARK 3 S21: 0.3660 S22: -0.0057 S23: 0.4192 REMARK 3 S31: 0.2737 S32: -0.2056 S33: -0.1473 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 98 A 132 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7130 24.2530 -12.3890 REMARK 3 T TENSOR REMARK 3 T11: 0.0732 T22: 0.1102 REMARK 3 T33: 0.1032 T12: 0.0012 REMARK 3 T13: -0.0725 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.0769 L22: 4.5974 REMARK 3 L33: 4.0003 L12: -0.2467 REMARK 3 L13: 0.2768 L23: -2.4069 REMARK 3 S TENSOR REMARK 3 S11: 0.2150 S12: 0.0252 S13: -0.2423 REMARK 3 S21: -0.1168 S22: -0.0248 S23: 0.1647 REMARK 3 S31: 0.1774 S32: 0.1512 S33: -0.1902 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 : A 133 A 183 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5420 27.0310 -6.7120 REMARK 3 T TENSOR REMARK 3 T11: 0.0788 T22: 0.1042 REMARK 3 T33: 0.0822 T12: -0.0095 REMARK 3 T13: -0.0337 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 1.7652 L22: 1.6461 REMARK 3 L33: 2.6231 L12: 0.1536 REMARK 3 L13: 0.2159 L23: -0.3465 REMARK 3 S TENSOR REMARK 3 S11: 0.1908 S12: -0.0714 S13: -0.2343 REMARK 3 S21: -0.0020 S22: -0.0119 S23: 0.1068 REMARK 3 S31: 0.0033 S32: -0.1016 S33: -0.1789 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 : A 184 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9200 40.4940 5.3420 REMARK 3 T TENSOR REMARK 3 T11: 0.2165 T22: 0.3745 REMARK 3 T33: 0.2204 T12: -0.0062 REMARK 3 T13: -0.0129 T23: -0.1602 REMARK 3 L TENSOR REMARK 3 L11: 5.9671 L22: 11.9672 REMARK 3 L33: 20.4537 L12: -2.6632 REMARK 3 L13: -9.6360 L23: -2.7408 REMARK 3 S TENSOR REMARK 3 S11: -0.1084 S12: 0.1583 S13: -0.0566 REMARK 3 S21: 0.5929 S22: -0.1466 S23: 0.0598 REMARK 3 S31: -0.3105 S32: -0.4619 S33: 0.2550 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4TNN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000201883. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000, DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15635 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.76700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXDE, MLPHARE, DM REMARK 200 STARTING MODEL: 1OEJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 UL OF 9.6 MG/ML PROTEIN IN 50MM REMARK 280 TRIS PH 7.9, 300 MM NACL AND 0.5MM TCEP WERE MIXED WITH 0.3 UL REMARK 280 OF THE SALTRX CONDITION #65 (2.5 M AMMONIUM SULFATE, 0.1 M BIS- REMARK 280 TRIS PROPANE PH 7.0) AND EQUILIBRATED AGAINST 1.5 M NACL IN MRC REMARK 280 2 DROPS 96 WELL CRYSTALLIZATION PLATE (SWISSCI), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.64800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.29600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 41.29600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.64800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 S SO4 A 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 353 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 362 LIES ON A SPECIAL POSITION. 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 HIS A 6 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 50 CD CE NZ REMARK 470 VAL A 54 CG1 CG2 REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 65 CE NZ REMARK 470 ASN A 98 CG OD1 ND2 REMARK 470 GLU A 99 CG CD OE1 OE2 REMARK 470 GLU A 132 CG CD OE1 OE2 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 O2 SO4 A 204 O HOH A 301 1.77 REMARK 500 O HOH A 352 O HOH A 414 2.08 REMARK 500 O HOH A 386 O HOH A 433 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 143 -159.23 -138.03 REMARK 500 ARG A 149 142.63 -173.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 207 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 1 N REMARK 620 2 HIS A 1 ND1 86.5 REMARK 620 3 HIS A 4 NE2 84.2 85.2 REMARK 620 4 HIS A 144 NE2 116.9 83.4 33.0 REMARK 620 5 HIS A 153 NE2 112.2 88.4 28.0 7.2 REMARK 620 6 HIS A 193 NE2 120.5 87.8 36.3 5.4 8.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 207 DBREF 4TNN A 1 193 UNP U6NCE6 U6NCE6_ECOLI 24 216 SEQRES 1 A 193 HIS GLY HIS HIS SER HIS GLY LYS PRO LEU THR GLU VAL SEQRES 2 A 193 GLU GLN LYS ALA ALA ASN GLY VAL PHE ASP ASP ALA ASN SEQRES 3 A 193 VAL GLN ASN ARG THR LEU SER ASP TRP ASP GLY VAL TRP SEQRES 4 A 193 GLN SER VAL TYR PRO LEU LEU GLN SER GLY LYS LEU ASP SEQRES 5 A 193 PRO VAL PHE GLN LYS LYS ALA ASP ALA ASP LYS THR LYS SEQRES 6 A 193 THR PHE ALA GLU ILE LYS ASP TYR TYR HIS LYS GLY TYR SEQRES 7 A 193 ALA THR ASP ILE GLU MET ILE GLY ILE GLU ASP GLY ILE SEQRES 8 A 193 VAL GLU PHE HIS ARG ASN ASN GLU THR THR SER CYS LYS SEQRES 9 A 193 TYR ASP TYR ASP GLY TYR LYS ILE LEU THR TYR LYS SER SEQRES 10 A 193 GLY LYS LYS GLY VAL ARG TYR LEU PHE GLU CYS LYS ASP SEQRES 11 A 193 PRO GLU SER LYS ALA PRO LYS TYR ILE GLN PHE SER ASP SEQRES 12 A 193 HIS ILE ILE ALA PRO ARG LYS SER SER HIS PHE HIS ILE SEQRES 13 A 193 PHE MET GLY ASN ASP SER GLN GLN SER LEU LEU ASN GLU SEQRES 14 A 193 MET GLU ASN TRP PRO THR TYR TYR PRO TYR GLN LEU SER SEQRES 15 A 193 SER GLU GLU VAL VAL GLU GLU MET MET SER HIS HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET NI A 207 1 HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION FORMUL 2 SO4 6(O4 S 2-) FORMUL 8 NI NI 2+ FORMUL 9 HOH *137(H2 O) HELIX 1 AA1 THR A 11 ASN A 19 1 9 HELIX 2 AA2 ASP A 23 VAL A 27 5 5 HELIX 3 AA3 THR A 31 ASP A 36 5 6 HELIX 4 AA4 VAL A 42 SER A 48 1 7 HELIX 5 AA5 LEU A 51 ASP A 62 1 12 HELIX 6 AA6 THR A 66 ALA A 79 1 14 HELIX 7 AA7 SER A 162 ASN A 168 1 7 HELIX 8 AA8 SER A 182 SER A 192 1 11 SHEET 1 AA1 9 THR A 100 LYS A 104 0 SHEET 2 AA1 9 ILE A 91 ARG A 96 -1 N PHE A 94 O THR A 101 SHEET 3 AA1 9 ILE A 82 GLU A 88 -1 N MET A 84 O HIS A 95 SHEET 4 AA1 9 GLY A 37 SER A 41 -1 N SER A 41 O GLU A 83 SHEET 5 AA1 9 THR A 175 PRO A 178 -1 O TYR A 177 N GLN A 40 SHEET 6 AA1 9 PHE A 154 GLY A 159 -1 N PHE A 154 O TYR A 176 SHEET 7 AA1 9 TYR A 138 SER A 142 -1 N GLN A 140 O PHE A 157 SHEET 8 AA1 9 LYS A 120 GLU A 127 -1 N PHE A 126 O ILE A 139 SHEET 9 AA1 9 ASP A 106 THR A 114 -1 N ASP A 108 O LEU A 125 SSBOND 1 CYS A 103 CYS A 128 1555 1555 2.13 LINK N HIS A 1 NI NI A 207 1555 2665 2.34 LINK ND1 HIS A 1 NI NI A 207 1555 2665 2.16 LINK NE2 HIS A 4 NI NI A 207 1555 2665 2.28 LINK NE2 HIS A 144 NI NI A 207 1555 1555 2.16 LINK NE2 HIS A 153 NI NI A 207 1555 1555 2.26 LINK NE2 HIS A 193 NI NI A 207 1555 1555 2.23 CISPEP 1 HIS A 1 GLY A 2 0 -6.61 CISPEP 2 HIS A 6 GLY A 7 0 -19.92 SITE 1 AC1 5 GLY A 7 LYS A 8 LYS A 116 ARG A 149 SITE 2 AC1 5 HOH A 303 SITE 1 AC2 4 ALA A 25 TYR A 43 GLN A 47 HIS A 75 SITE 1 AC3 4 GLN A 56 THR A 66 PHE A 67 HOH A 395 SITE 1 AC4 4 SER A 165 ASN A 168 HOH A 301 HOH A 311 SITE 1 AC5 3 THR A 11 GLU A 12 HOH A 412 SITE 1 AC6 6 THR A 31 SER A 33 HOH A 321 HOH A 333 SITE 2 AC6 6 HOH A 346 HOH A 359 SITE 1 AC7 5 HIS A 1 HIS A 4 HIS A 144 HIS A 153 SITE 2 AC7 5 HIS A 193 CRYST1 76.583 76.583 61.944 90.00 90.00 120.00 P 31 2 1 6 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 0.013058 0.007539 0.000000 0.00000 SCALE2 0.000000 0.015078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016144 0.00000