HEADER ISOMERASE 14-OCT-16 5TNV TITLE CRYSTAL STRUCTURE OF A XYLOSE ISOMERASE-LIKE TIM BARREL PROTEIN FROM TITLE 2 MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP ENDONUCLEASE, FAMILY PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLOSE ISOMERASE-LIKE TIM BARREL; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: MSMEG_6790, MSMEI_6607; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS XYLOSE ISOMERASE-LIKE TIM BARREL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.J.COOK,A.A.FEDOROV,E.V.FEDOROV,H.HUANG,J.B.BONANNO,J.A.GERLT, AUTHOR 2 S.C.ALMO REVDAT 6 06-MAR-24 5TNV 1 REMARK REVDAT 5 25-DEC-19 5TNV 1 REMARK REVDAT 4 27-SEP-17 5TNV 1 REMARK REVDAT 3 03-MAY-17 5TNV 1 AUTHOR JRNL REVDAT 2 18-JAN-17 5TNV 1 AUTHOR JRNL REVDAT 1 09-NOV-16 5TNV 0 JRNL AUTH W.J.COOK,A.A.FEDOROV,E.V.FEDOROV,H.HUANG,J.B.BONANNO, JRNL AUTH 2 J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF A XYLOSE ISOMERASE-LIKE TIM BARREL JRNL TITL 2 PROTEIN FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH JRNL TITL 3 MAGNESIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL 2016/4 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7456 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 143142 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.103 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.126 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 6441 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 122537 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2399 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 432 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2828.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2313.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 25767 REMARK 3 NUMBER OF RESTRAINTS : 31527 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.375 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.036 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.118 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS BY SIRAS REMARK 3 USING THE SHELXC/D/E SUITE OF PROGRAMS. THE THREE MERCURY SITES REMARK 3 WERE LOCATED WITH SHELXD. PHASING, DENSITY MODIFICATION AND REMARK 3 INITIAL CHAIN TRACING WERE DONE WITH SHELXE REMARK 4 REMARK 4 5TNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DIAMOND REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 150741 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 29.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXCD 3.3.22 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE; 25% PEG-3350, REMARK 280 0.1 M HEPES; 5 MM MG, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.43450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.92222 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.73933 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 41.43450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.92222 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.73933 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 41.43450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.92222 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.73933 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.84444 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 83.47867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 47.84444 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 83.47867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 47.84444 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 83.47867 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 82.86900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 41.43450 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 71.76666 REMARK 350 BIOMT3 3 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 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 760 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 894 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER 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 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 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 MET A 1 CG SD CE 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 C THR A 86 H ARG A 87 1.18 REMARK 500 HG SER A 218 O HOH A 503 1.48 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 68 CD GLU A 68 OE1 -0.081 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 HIS A 5 CA - CB - CG ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 THR A 86 CA - C - N ANGL. DEV. = 14.1 DEGREES REMARK 500 THR A 86 O - C - N ANGL. DEV. = -20.2 DEGREES REMARK 500 THR A 86 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 87 C - N - CA ANGL. DEV. = 29.2 DEGREES REMARK 500 ARG A 87 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 150 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 157 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 GLU A 158 OE1 - CD - OE2 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 164 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 212 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 212 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = -3.3 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 THR A 52 -163.92 58.95 REMARK 500 TRP A 55 -129.41 -119.56 REMARK 500 THR A 86 -121.50 -102.10 REMARK 500 ARG A 87 52.57 -59.33 REMARK 500 PRO A 253 151.64 -47.09 REMARK 500 HIS A 281 93.77 -164.63 REMARK 500 SER A 284 -153.02 55.17 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 930 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 931 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 932 DISTANCE = 6.46 ANGSTROMS 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 173 OE2 REMARK 620 2 ASP A 203 OD2 106.4 REMARK 620 3 GLU A 280 OE2 154.4 88.3 REMARK 620 4 HOH A 501 O 107.3 118.6 47.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 DBREF 5TNV A 1 306 UNP A0R760 A0R760_MYCS2 1 306 SEQADV 5TNV MET A -19 UNP A0R760 INITIATING METHIONINE SEQADV 5TNV GLY A -18 UNP A0R760 EXPRESSION TAG SEQADV 5TNV SER A -17 UNP A0R760 EXPRESSION TAG SEQADV 5TNV SER A -16 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -15 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -14 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -13 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -12 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -11 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A -10 UNP A0R760 EXPRESSION TAG SEQADV 5TNV SER A -9 UNP A0R760 EXPRESSION TAG SEQADV 5TNV SER A -8 UNP A0R760 EXPRESSION TAG SEQADV 5TNV GLY A -7 UNP A0R760 EXPRESSION TAG SEQADV 5TNV LEU A -6 UNP A0R760 EXPRESSION TAG SEQADV 5TNV VAL A -5 UNP A0R760 EXPRESSION TAG SEQADV 5TNV PRO A -4 UNP A0R760 EXPRESSION TAG SEQADV 5TNV ARG A -3 UNP A0R760 EXPRESSION TAG SEQADV 5TNV GLY A -2 UNP A0R760 EXPRESSION TAG SEQADV 5TNV SER A -1 UNP A0R760 EXPRESSION TAG SEQADV 5TNV HIS A 0 UNP A0R760 EXPRESSION TAG SEQRES 1 A 326 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 326 LEU VAL PRO ARG GLY SER HIS MET TYR SER ALA HIS THR SEQRES 3 A 326 TRP PRO ILE ALA ALA ASN MET LEU GLY PHE GLY ASN ARG SEQRES 4 A 326 ALA PRO ASP GLY GLY HIS ILE LYS ASP ALA PRO ALA GLY SEQRES 5 A 326 VAL TRP ALA LYS GLN LEU ARG GLN VAL ARG GLU LEU GLY SEQRES 6 A 326 PHE ASP HIS ILE ASP PRO THR ASP ALA TRP VAL PRO LEU SEQRES 7 A 326 ALA ALA LEU SER ASP SER ARG ILE GLU GLU PHE ARG THR SEQRES 8 A 326 VAL LEU ALA ASP GLU GLY LEU ALA ILE SER SER ILE SER SEQRES 9 A 326 MET THR ARG SER SER ILE VAL ASP VAL GLU ASN GLY GLU SEQRES 10 A 326 LYS ASN LEU ALA ASP ALA HIS ARG LEU ILE ASP LEU ALA SEQRES 11 A 326 PRO SER PHE GLY ALA THR ILE VAL ASN THR GLY PHE MET SEQRES 12 A 326 GLN ALA LEU THR PRO GLU GLN GLU LYS GLN ILE TRP PHE SEQRES 13 A 326 TRP LEU VAL GLN GLY HIS VAL ASP ASP PRO ALA LEU ARG SEQRES 14 A 326 ASP LEU ALA ILE GLU ARG VAL ARG GLU LEU GLY ASP HIS SEQRES 15 A 326 ALA ARG THR ASN GLY ILE GLN LEU SER LEU GLU MET TYR SEQRES 16 A 326 GLU ASP THR TYR ILE GLY THR PRO ASP ASP ALA VAL ALA SEQRES 17 A 326 PHE ILE LYS ASP VAL ASP HIS ASP ALA VAL GLY LEU ASN SEQRES 18 A 326 PRO ASP LEU GLY ASN LEU VAL ARG LEU HIS ARG PRO MET SEQRES 19 A 326 PRO HIS PRO SER GLU MET TYR ALA LYS VAL LEU PRO TYR SEQRES 20 A 326 SER ASN PHE TRP HIS ILE LYS ASN TYR SER ARG ASP PHE SEQRES 21 A 326 ASP PRO ALA THR GLY ALA TYR SER SER ALA PRO LEU PRO SEQRES 22 A 326 LEU LYS TYR GLY TYR VAL ASN TYR ARG GLN ILE ILE ARG SEQRES 23 A 326 LEU ALA LEU GLU LEU GLY TYR THR GLY PRO PHE CYS CYS SEQRES 24 A 326 GLU HIS TYR GLY SER ASP SER LEU GLY VAL CYS ALA GLU SEQRES 25 A 326 ASN ARG GLU TYR ILE LEU GLN VAL LEU THR SER ALA LEU SEQRES 26 A 326 ALA HET MG A 401 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *432(H2 O) HELIX 1 AA1 SER A 3 TRP A 7 5 5 HELIX 2 AA2 LEU A 14 GLY A 17 5 4 HELIX 3 AA3 HIS A 25 ALA A 29 5 5 HELIX 4 AA4 PRO A 30 LEU A 44 1 15 HELIX 5 AA5 PRO A 57 LEU A 61 5 5 HELIX 6 AA6 SER A 62 GLU A 76 1 15 HELIX 7 AA7 ASN A 95 ALA A 110 1 16 HELIX 8 AA8 PRO A 111 GLY A 114 5 4 HELIX 9 AA9 THR A 127 GLN A 133 1 7 HELIX 10 AB1 TRP A 135 VAL A 139 5 5 HELIX 11 AB2 ASP A 145 ALA A 147 5 3 HELIX 12 AB3 LEU A 148 ASN A 166 1 19 HELIX 13 AB4 THR A 182 ASP A 194 1 13 HELIX 14 AB5 LEU A 204 ARG A 209 1 6 HELIX 15 AB6 HIS A 216 LEU A 225 1 10 HELIX 16 AB7 PRO A 226 SER A 228 5 3 HELIX 17 AB8 PRO A 253 GLY A 257 5 5 HELIX 18 AB9 ASN A 260 LEU A 271 1 12 HELIX 19 AC1 ASP A 285 ALA A 306 1 22 SHEET 1 AA1 5 ALA A 79 ILE A 80 0 SHEET 2 AA1 5 HIS A 48 ASP A 50 1 N ILE A 49 O ALA A 79 SHEET 3 AA1 5 ILE A 9 ASN A 12 1 N ALA A 11 O ASP A 50 SHEET 4 AA1 5 PHE A 277 CYS A 279 1 O CYS A 279 N ALA A 10 SHEET 5 AA1 5 TRP A 231 HIS A 232 1 N TRP A 231 O CYS A 278 SHEET 1 AA2 4 SER A 82 SER A 84 0 SHEET 2 AA2 4 ILE A 117 GLY A 121 1 O ASN A 119 N ILE A 83 SHEET 3 AA2 4 GLN A 169 GLU A 173 1 O SER A 171 N THR A 120 SHEET 4 AA2 4 VAL A 198 ASN A 201 1 O ASN A 201 N LEU A 172 SHEET 1 AA3 2 ASN A 235 PHE A 240 0 SHEET 2 AA3 2 TYR A 247 LEU A 252 -1 O ALA A 250 N SER A 237 LINK OE2 GLU A 173 MG MG A 401 1555 1555 1.97 LINK OD2 ASP A 203 MG MG A 401 1555 1555 1.97 LINK OE2BGLU A 280 MG MG A 401 1555 1555 2.02 LINK MG MG A 401 O HOH A 501 1555 1555 1.72 SITE 1 AC1 5 GLU A 173 ASP A 203 HIS A 232 GLU A 280 SITE 2 AC1 5 HOH A 501 CRYST1 82.869 82.869 125.218 90.00 90.00 120.00 H 3 9 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 0.012067 0.006967 0.000000 0.00000 SCALE2 0.000000 0.013934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007986 0.00000