HEADER DNA BINDING PROTEIN 27-DEC-04 1YDX TITLE CRYSTAL STRUCTURE OF TYPE-I RESTRICTION-MODIFICATION SYSTEM S SUBUNIT TITLE 2 FROM M. GENITALIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE I RESTRICTION ENZYME SPECIFICITY PROTEIN MG438; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE I RESTRICTION-MODIFICATION SYSTEM SPECIFICITY SUBUNIT, COMPND 5 S PROTEIN, S.MGEORF438P; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM; SOURCE 3 ORGANISM_TAXID: 2097; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET19B KEYWDS TYPE-I HSDS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.MACHADO,O.QUIJADA,J.PINOL,I.FITA,E.QUEROL,X.CARPENA REVDAT 3 13-JUL-11 1YDX 1 VERSN REVDAT 2 24-FEB-09 1YDX 1 VERSN REVDAT 1 23-AUG-05 1YDX 0 JRNL AUTH B.M.CALISTO,O.Q.PICH,J.PINOL,I.FITA,E.QUEROL,X.CARPENA JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE TYPE I JRNL TITL 2 RESTRICTION-MODIFICATION S SUBUNIT FROM MYCOPLASMA JRNL TITL 3 GENITALIUM JRNL REF J.MOL.BIOL. V. 351 749 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16038930 JRNL DOI 10.1016/J.JMB.2005.06.050 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25685 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.231 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1842 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.55000 REMARK 3 B22 (A**2) : 1.55000 REMARK 3 B33 (A**2) : -2.32000 REMARK 3 B12 (A**2) : -0.77000 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): 0.227 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.703 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3091 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4158 ; 1.541 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 371 ; 6.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;38.326 ;25.034 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 588 ;18.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;13.005 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 456 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2294 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1206 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2046 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 128 ; 0.150 ; 0.200 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): 49 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.165 ; 0.200 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): 1937 ; 0.817 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2994 ; 1.279 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1338 ; 2.292 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1164 ; 3.413 ; 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 : 6 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 142 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8320 60.7110 -1.4840 REMARK 3 T TENSOR REMARK 3 T11: -0.2416 T22: -0.2690 REMARK 3 T33: 0.0807 T12: 0.0177 REMARK 3 T13: 0.0157 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 4.6829 L22: 2.4440 REMARK 3 L33: 2.8757 L12: -0.1692 REMARK 3 L13: -1.7031 L23: -0.3958 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: 0.1488 S13: 0.0779 REMARK 3 S21: -0.0762 S22: -0.0685 S23: 0.3187 REMARK 3 S31: -0.0220 S32: -0.1886 S33: 0.0322 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 143 A 183 REMARK 3 ORIGIN FOR THE GROUP (A): 18.7360 40.6280 8.8060 REMARK 3 T TENSOR REMARK 3 T11: -0.1821 T22: -0.1518 REMARK 3 T33: 0.0708 T12: -0.0580 REMARK 3 T13: 0.0125 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 1.3827 L22: 14.4556 REMARK 3 L33: 20.4725 L12: 3.5430 REMARK 3 L13: -4.4838 L23: -16.8815 REMARK 3 S TENSOR REMARK 3 S11: -0.1405 S12: 0.1757 S13: -0.0269 REMARK 3 S21: -0.4181 S22: 0.7007 S23: 0.3818 REMARK 3 S31: 0.6712 S32: -1.1455 S33: -0.5601 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 184 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): 27.0370 36.5610 33.9140 REMARK 3 T TENSOR REMARK 3 T11: -0.1119 T22: -0.1452 REMARK 3 T33: 0.1621 T12: -0.0631 REMARK 3 T13: 0.0280 T23: 0.0830 REMARK 3 L TENSOR REMARK 3 L11: 4.7834 L22: 3.3884 REMARK 3 L33: 6.6375 L12: 1.6945 REMARK 3 L13: 0.2536 L23: -0.1496 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: 0.0000 S13: 0.2351 REMARK 3 S21: -0.1027 S22: 0.0723 S23: 0.0048 REMARK 3 S31: -0.6123 S32: 0.4368 S33: -0.0794 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 330 A 370 REMARK 3 ORIGIN FOR THE GROUP (A): 25.9780 40.0510 14.8150 REMARK 3 T TENSOR REMARK 3 T11: -0.1331 T22: -0.1355 REMARK 3 T33: 0.1141 T12: 0.0180 REMARK 3 T13: 0.0231 T23: -0.0486 REMARK 3 L TENSOR REMARK 3 L11: 0.1478 L22: 14.7493 REMARK 3 L33: 8.6444 L12: 1.0373 REMARK 3 L13: -0.8845 L23: -11.2107 REMARK 3 S TENSOR REMARK 3 S11: -0.0845 S12: -0.1156 S13: -0.1146 REMARK 3 S21: -0.1892 S22: -0.1041 S23: -0.3555 REMARK 3 S31: 0.4037 S32: 0.0349 S33: 0.1886 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 371 A 374 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1490 71.6780 1.2640 REMARK 3 T TENSOR REMARK 3 T11: 0.0927 T22: 0.0710 REMARK 3 T33: 0.3735 T12: 0.0169 REMARK 3 T13: 0.1481 T23: -0.0371 REMARK 3 L TENSOR REMARK 3 L11: 38.7972 L22: 15.8783 REMARK 3 L33: 48.7431 L12: -7.3093 REMARK 3 L13: -22.0858 L23: 23.1263 REMARK 3 S TENSOR REMARK 3 S11: -1.5062 S12: -3.0089 S13: 1.4981 REMARK 3 S21: 1.0347 S22: 0.8982 S23: 0.3538 REMARK 3 S31: 0.3349 S32: 1.8114 S33: 0.6080 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 386 A 514 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1710 52.7430 8.5270 REMARK 3 T TENSOR REMARK 3 T11: -0.1308 T22: -0.1450 REMARK 3 T33: 0.1572 T12: -0.0163 REMARK 3 T13: 0.0370 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.3620 L22: 0.4775 REMARK 3 L33: 0.3961 L12: 0.0368 REMARK 3 L13: -0.0262 L23: -0.3591 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: -0.1186 S13: 0.0096 REMARK 3 S21: 0.0652 S22: -0.0270 S23: 0.0718 REMARK 3 S31: -0.0170 S32: 0.0031 S33: -0.0064 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1YDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935, 0.97950, 0.97565, REMARK 200 0.97930 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30905 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 58.28233 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 116.56467 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 116.56467 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 58.28233 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 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 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 MSE A -22 REMARK 465 GLY A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 ILE A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 LYS A -1 REMARK 465 HIS A 0 REMARK 465 GLU A 375 REMARK 465 ARG A 376 REMARK 465 THR A 377 REMARK 465 LYS A 378 REMARK 465 SER A 379 REMARK 465 ILE A 380 REMARK 465 LYS A 381 REMARK 465 ASP A 382 REMARK 465 TYR A 383 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 152 C LEU A 153 N 0.148 REMARK 500 LYS A 219 C SER A 220 N 0.178 REMARK 500 GLU A 221 CD GLU A 221 OE1 0.088 REMARK 500 ARG A 223 CD ARG A 223 NE 0.168 REMARK 500 ARG A 223 NE ARG A 223 CZ 0.174 REMARK 500 ARG A 223 CZ ARG A 223 NH1 0.180 REMARK 500 ARG A 223 CZ ARG A 223 NH2 0.166 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 223 CD - NE - CZ ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG A 223 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 223 NE - CZ - NH2 ANGL. DEV. = -11.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 45 -107.47 -115.55 REMARK 500 TYR A 217 113.61 95.46 REMARK 500 ALA A 234 -23.83 168.57 REMARK 500 ASP A 310 -97.92 -58.50 REMARK 500 SER A 312 36.85 80.58 REMARK 500 PRO A 313 -138.02 -107.97 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 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 385 DBREF 1YDX A 1 383 UNP Q49434 T1SX_MYCGE 1 383 SEQADV 1YDX MSE A -22 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX GLY A -21 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -20 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -19 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -18 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -17 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -16 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -15 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -14 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -13 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -12 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -11 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX SER A -10 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX SER A -9 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX GLY A -8 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A -7 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX ILE A -6 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX ASP A -5 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX ASP A -4 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX ASP A -3 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX ASP A -2 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX LYS A -1 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX HIS A 0 UNP Q49434 CLONING ARTIFACT SEQADV 1YDX MSE A 1 UNP Q49434 MET 1 MODIFIED RESIDUE SEQADV 1YDX MSE A 29 UNP Q49434 MET 29 MODIFIED RESIDUE SEQADV 1YDX MSE A 201 UNP Q49434 MET 201 MODIFIED RESIDUE SEQADV 1YDX MSE A 283 UNP Q49434 MET 283 MODIFIED RESIDUE SEQADV 1YDX MSE A 307 UNP Q49434 MET 307 MODIFIED RESIDUE SEQADV 1YDX MSE A 373 UNP Q49434 MET 373 MODIFIED RESIDUE SEQRES 1 A 406 MSE GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 406 SER GLY HIS ILE ASP ASP ASP ASP LYS HIS MSE THR PRO SEQRES 3 A 406 LYS LEU LYS LEU ASN ASN ASN ILE ASN TRP THR LYS ARG SEQRES 4 A 406 THR ILE ASP SER LEU PHE ASP LEU LYS LYS GLY GLU MSE SEQRES 5 A 406 LEU GLU LYS GLU LEU ILE THR PRO GLU GLY LYS TYR GLU SEQRES 6 A 406 TYR PHE ASN GLY GLY VAL LYS ASN SER GLY ARG THR ASP SEQRES 7 A 406 LYS PHE ASN THR PHE LYS ASN THR ILE SER VAL ILE VAL SEQRES 8 A 406 GLY GLY SER CYS GLY TYR VAL ARG LEU ALA ASP LYS ASN SEQRES 9 A 406 PHE PHE CYS GLY GLN SER ASN CYS THR LEU ASN LEU LEU SEQRES 10 A 406 ASP PRO LEU GLU LEU ASP LEU LYS PHE ALA TYR TYR ALA SEQRES 11 A 406 LEU LYS SER GLN GLN GLU ARG ILE GLU ALA LEU ALA PHE SEQRES 12 A 406 GLY THR THR ILE GLN ASN ILE ARG ILE SER ASP LEU LYS SEQRES 13 A 406 GLU LEU GLU ILE PRO PHE THR SER ASN LYS ASN GLU GLN SEQRES 14 A 406 HIS ALA ILE ALA ASN THR LEU SER VAL PHE ASP GLU ARG SEQRES 15 A 406 LEU GLU ASN LEU ALA SER LEU ILE GLU ILE ASN ARG LYS SEQRES 16 A 406 LEU ARG ASP GLU TYR ALA HIS LYS LEU PHE SER LEU ASP SEQRES 17 A 406 GLU ALA PHE LEU SER HIS TRP LYS LEU GLU ALA LEU GLN SEQRES 18 A 406 SER GLN MSE HIS GLU ILE THR LEU GLY GLU ILE PHE ASN SEQRES 19 A 406 PHE LYS SER GLY LYS TYR LEU LYS SER GLU GLU ARG LEU SEQRES 20 A 406 GLU GLU GLY LYS PHE PRO TYR TYR GLY ALA GLY ILE ASP SEQRES 21 A 406 ASN THR GLY PHE VAL ALA GLU PRO ASN THR GLU LYS ASP SEQRES 22 A 406 THR ILE SER ILE ILE SER ASN GLY TYR SER LEU GLY ASN SEQRES 23 A 406 ILE ARG TYR HIS GLU ILE PRO TRP PHE ASN GLY THR GLY SEQRES 24 A 406 SER ILE ALA LEU GLU PRO MSE ASN ASN GLU ILE TYR VAL SEQRES 25 A 406 PRO PHE PHE TYR CYS ALA LEU LYS TYR LEU GLN LYS ASP SEQRES 26 A 406 ILE LYS GLU ARG MSE LYS SER ASP ASP SER PRO PHE LEU SEQRES 27 A 406 SER LEU LYS LEU ALA GLY GLU ILE LYS VAL PRO TYR VAL SEQRES 28 A 406 LYS SER PHE GLN LEU GLN ARG LYS ALA GLY LYS ILE VAL SEQRES 29 A 406 PHE LEU LEU ASP GLN LYS LEU ASP GLN TYR LYS LYS GLU SEQRES 30 A 406 LEU SER SER LEU THR VAL ILE ARG ASP THR LEU LEU LYS SEQRES 31 A 406 LYS LEU PHE PRO ASP MSE THR GLU ARG THR LYS SER ILE SEQRES 32 A 406 LYS ASP TYR MODRES 1YDX MSE A 1 MET SELENOMETHIONINE MODRES 1YDX MSE A 29 MET SELENOMETHIONINE MODRES 1YDX MSE A 201 MET SELENOMETHIONINE MODRES 1YDX MSE A 283 MET SELENOMETHIONINE MODRES 1YDX MSE A 307 MET SELENOMETHIONINE MODRES 1YDX MSE A 373 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 29 8 HET MSE A 201 8 HET MSE A 283 8 HET MSE A 307 8 HET MSE A 373 8 HET CL A 384 1 HET CL A 385 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *129(H2 O) HELIX 1 1 ILE A 18 LEU A 21 1 4 HELIX 2 2 GLU A 31 ILE A 35 5 5 HELIX 3 3 ASP A 100 SER A 110 1 11 HELIX 4 4 GLN A 111 ALA A 117 1 7 HELIX 5 5 ARG A 128 LEU A 135 1 8 HELIX 6 6 ASN A 142 SER A 183 1 42 HELIX 7 7 ASP A 185 TRP A 192 1 8 HELIX 8 8 GLU A 195 MSE A 201 1 7 HELIX 9 9 LYS A 219 ARG A 223 5 5 HELIX 10 10 TYR A 288 ASP A 311 1 24 HELIX 11 11 SER A 316 GLU A 322 1 7 HELIX 12 12 SER A 330 PHE A 370 1 41 SHEET 1 A 2 THR A 14 THR A 17 0 SHEET 2 A 2 GLU A 136 PHE A 139 -1 O PHE A 139 N THR A 14 SHEET 1 B 4 PHE A 22 LYS A 26 0 SHEET 2 B 4 ASN A 88 LEU A 93 -1 O ASN A 92 N ASP A 23 SHEET 3 B 4 ILE A 64 ILE A 67 -1 N ILE A 64 O LEU A 91 SHEET 4 B 4 VAL A 75 LEU A 77 -1 O ARG A 76 N SER A 65 SHEET 1 C 3 ARG A 53 THR A 54 0 SHEET 2 C 3 TYR A 41 PHE A 44 -1 N TYR A 41 O THR A 54 SHEET 3 C 3 PHE A 83 CYS A 84 1 O PHE A 83 N GLU A 42 SHEET 1 D 2 HIS A 202 THR A 205 0 SHEET 2 D 2 LYS A 324 TYR A 327 -1 O VAL A 325 N ILE A 204 SHEET 1 E 4 PHE A 210 SER A 214 0 SHEET 2 E 4 SER A 277 PRO A 282 -1 O ALA A 279 N LYS A 213 SHEET 3 E 4 THR A 251 ILE A 255 -1 N ILE A 252 O LEU A 280 SHEET 4 E 4 ILE A 264 HIS A 267 -1 O HIS A 267 N THR A 251 SHEET 1 F 3 PHE A 241 VAL A 242 0 SHEET 2 F 3 PHE A 229 TYR A 232 -1 N PHE A 229 O VAL A 242 SHEET 3 F 3 PHE A 272 ASN A 273 1 O PHE A 272 N PRO A 230 LINK C MSE A 1 N THR A 2 1555 1555 1.34 LINK C GLU A 28 N MSE A 29 1555 1555 1.32 LINK C MSE A 29 N LEU A 30 1555 1555 1.33 LINK C GLN A 200 N MSE A 201 1555 1555 1.33 LINK C MSE A 201 N HIS A 202 1555 1555 1.34 LINK C PRO A 282 N MSE A 283 1555 1555 1.33 LINK C MSE A 283 N ASN A 284 1555 1555 1.33 LINK C ARG A 306 N MSE A 307 1555 1555 1.34 LINK C MSE A 307 N LYS A 308 1555 1555 1.33 LINK C ASP A 372 N MSE A 373 1555 1555 1.34 LINK C MSE A 373 N THR A 374 1555 1555 1.33 SITE 1 AC1 3 THR A 122 THR A 123 ILE A 124 SITE 1 AC2 2 GLN A 300 LYS A 304 CRYST1 76.601 76.601 174.847 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 0.013055 0.007537 0.000000 0.00000 SCALE2 0.000000 0.015074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005719 0.00000 HETATM 1 N MSE A 1 28.526 73.639 -5.637 1.00 54.29 N HETATM 2 CA MSE A 1 27.916 72.313 -5.996 1.00 54.54 C HETATM 3 C MSE A 1 29.014 71.241 -6.237 1.00 53.35 C HETATM 4 O MSE A 1 29.153 70.704 -7.368 1.00 53.82 O HETATM 5 CB MSE A 1 27.005 72.449 -7.238 1.00 55.84 C HETATM 6 CG MSE A 1 25.688 73.307 -7.093 1.00 57.50 C HETATM 7 SE MSE A 1 24.238 72.319 -6.229 0.70 64.08 SE HETATM 8 CE MSE A 1 24.580 73.041 -4.367 1.00 61.55 C