HEADER LYASE 27-APR-07 2UZH TITLE MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE TITLE 2 SYNTHASE (ISPF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 4.6.1.12; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: EACH CONTAINS A ZN CATION, WHICH IS REQUIRED FOR COMPND 7 ACTIVITY, AND CDP, A FRAGMENT OF SUBSTRATE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 1772; SOURCE 4 STRAIN: MC(2)155; SOURCE 5 ATCC: 700084; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15TEV (VARIANT OF PET15B FROM NOVAGEN) KEYWDS ISPF, LYASE, MYCOBACTERIA, COMPLEX WITH CDP, NON-MEVALONATE PATHWAY KEYWDS 2 OF ISOPRENOID BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR L.BUETOW,A.C.BROWN,T.PARISH,W.N.HUNTER REVDAT 3 13-DEC-23 2UZH 1 LINK REVDAT 2 24-FEB-09 2UZH 1 VERSN REVDAT 1 06-NOV-07 2UZH 0 JRNL AUTH L.BUETOW,A.C.BROWN,T.PARISH,W.N.HUNTER JRNL TITL THE STRUCTURE OF MYCOBACTERIA JRNL TITL 2 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE, AN JRNL TITL 3 ESSENTIAL ENZYME, PROVIDES A PLATFORM FOR DRUG DISCOVERY. JRNL REF BMC STRUCT.BIOL. V. 7 68 2007 JRNL REFN ESSN 1472-6807 JRNL PMID 17956607 JRNL DOI 10.1186/1472-6807-7-68 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31702 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1671 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1842 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3275 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : 0.00000 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): 0.179 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.085 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3677 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5056 ; 1.570 ; 2.042 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 6.267 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;35.135 ;23.662 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 535 ;17.500 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;22.030 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 613 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2741 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1765 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2455 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.178 ; 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): 53 ; 0.181 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.211 ; 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): 2400 ; 2.488 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3727 ; 3.633 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1403 ; 2.669 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1303 ; 3.923 ; 3.000 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 : NULL 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 2UZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-06 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8730 REMARK 200 MONOCHROMATOR : HORIZONTALLY SIDE DIFFRACTING REMARK 200 SILICON 111 CRYSTAL REMARK 200 OPTICS : PT COATED MIRRORS IN A REMARK 200 KIRKPATRICK-BAEZ (KB) GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33193 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 51.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 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) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1GX1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.1 M SODIUM CACODYLATE REMARK 280 PH 6.5, 0.2 M CALCIUM ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 79.56050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.56050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.08000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 79.56050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.56050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.08000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 79.56050 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 79.56050 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 27.08000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 79.56050 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 79.56050 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 27.08000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 GLY A 36 REMARK 465 HIS A 37 REMARK 465 PRO A 158 REMARK 465 VAL A 159 REMARK 465 GLY A 160 REMARK 465 ASP A 161 REMARK 465 ALA A 162 REMARK 465 LYS A 163 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 MET B 2 REMARK 465 GLY B 36 REMARK 465 HIS B 37 REMARK 465 PRO B 158 REMARK 465 VAL B 159 REMARK 465 GLY B 160 REMARK 465 ASP B 161 REMARK 465 ALA B 162 REMARK 465 LYS B 163 REMARK 465 GLY C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 MET C 2 REMARK 465 PRO C 158 REMARK 465 VAL C 159 REMARK 465 GLY C 160 REMARK 465 ASP C 161 REMARK 465 ALA C 162 REMARK 465 LYS C 163 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 30 -64.84 -166.10 REMARK 500 ASP A 67 43.98 38.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 29 ASP A 30 -136.13 REMARK 500 ALA C 156 GLU C 157 38.05 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 B2019 DISTANCE = 6.38 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 ZN A1157 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 11 OD2 REMARK 620 2 HIS A 13 NE2 98.7 REMARK 620 3 HIS A 45 ND1 95.8 119.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1157 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 11 OD1 REMARK 620 2 HIS B 13 NE2 96.8 REMARK 620 3 HIS B 45 ND1 129.2 118.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1157 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 11 OD2 REMARK 620 2 HIS C 13 NE2 93.2 REMARK 620 3 HIS C 45 ND1 93.2 123.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDP A1158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDP B1158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDP C1158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPE B1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1162 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1162 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1163 REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST TWO AMINO ACIDS OF SEQUENCE CORRESPOND TO REMNANTS REMARK 999 OF THE 6XHIS TAG. DBREF 2UZH A -1 0 PDB 2UZH 2UZH -1 0 DBREF 2UZH A 1 163 UNP A0R559 A0R559_MYCS2 1 163 DBREF 2UZH B -1 0 PDB 2UZH 2UZH -1 0 DBREF 2UZH B 1 163 UNP A0R559 A0R559_MYCS2 1 163 DBREF 2UZH C -1 0 PDB 2UZH 2UZH -1 0 DBREF 2UZH C 1 163 UNP A0R559 A0R559_MYCS2 1 163 SEQRES 1 A 165 GLY HIS MET MET LEU PRO ARG VAL GLY LEU GLY THR ASP SEQRES 2 A 165 VAL HIS PRO ILE GLU ALA GLY ARG PRO CYS ARG LEU LEU SEQRES 3 A 165 CYS LEU GLU PHE ASP ASP ALA ASP GLY CYS ALA GLY HIS SEQRES 4 A 165 SER ASP GLY ASP VAL ALA ALA HIS ALA LEU CYS ASP ALA SEQRES 5 A 165 LEU LEU SER ALA ALA GLY LEU GLY ASP LEU GLY THR ILE SEQRES 6 A 165 PHE GLY THR ASP ARG PRO GLN TRP ARG GLY ALA SER GLY SEQRES 7 A 165 ALA ASP MET ILE ARG HIS VAL ARG GLY LEU VAL GLU ASN SEQRES 8 A 165 ALA GLY PHE VAL ILE GLY ASN ALA THR VAL GLN VAL ILE SEQRES 9 A 165 GLY ASN ARG PRO LYS VAL GLY PRO ARG ARG GLU GLU ALA SEQRES 10 A 165 GLN GLN VAL LEU SER GLU LEU VAL GLY ALA PRO VAL SER SEQRES 11 A 165 VAL SER ALA THR THR THR ASP GLY LEU GLY LEU THR GLY SEQRES 12 A 165 ARG GLY GLU GLY LEU ALA ALA ILE ALA THR ALA LEU VAL SEQRES 13 A 165 ALA ALA GLU PRO VAL GLY ASP ALA LYS SEQRES 1 B 165 GLY HIS MET MET LEU PRO ARG VAL GLY LEU GLY THR ASP SEQRES 2 B 165 VAL HIS PRO ILE GLU ALA GLY ARG PRO CYS ARG LEU LEU SEQRES 3 B 165 CYS LEU GLU PHE ASP ASP ALA ASP GLY CYS ALA GLY HIS SEQRES 4 B 165 SER ASP GLY ASP VAL ALA ALA HIS ALA LEU CYS ASP ALA SEQRES 5 B 165 LEU LEU SER ALA ALA GLY LEU GLY ASP LEU GLY THR ILE SEQRES 6 B 165 PHE GLY THR ASP ARG PRO GLN TRP ARG GLY ALA SER GLY SEQRES 7 B 165 ALA ASP MET ILE ARG HIS VAL ARG GLY LEU VAL GLU ASN SEQRES 8 B 165 ALA GLY PHE VAL ILE GLY ASN ALA THR VAL GLN VAL ILE SEQRES 9 B 165 GLY ASN ARG PRO LYS VAL GLY PRO ARG ARG GLU GLU ALA SEQRES 10 B 165 GLN GLN VAL LEU SER GLU LEU VAL GLY ALA PRO VAL SER SEQRES 11 B 165 VAL SER ALA THR THR THR ASP GLY LEU GLY LEU THR GLY SEQRES 12 B 165 ARG GLY GLU GLY LEU ALA ALA ILE ALA THR ALA LEU VAL SEQRES 13 B 165 ALA ALA GLU PRO VAL GLY ASP ALA LYS SEQRES 1 C 165 GLY HIS MET MET LEU PRO ARG VAL GLY LEU GLY THR ASP SEQRES 2 C 165 VAL HIS PRO ILE GLU ALA GLY ARG PRO CYS ARG LEU LEU SEQRES 3 C 165 CYS LEU GLU PHE ASP ASP ALA ASP GLY CYS ALA GLY HIS SEQRES 4 C 165 SER ASP GLY ASP VAL ALA ALA HIS ALA LEU CYS ASP ALA SEQRES 5 C 165 LEU LEU SER ALA ALA GLY LEU GLY ASP LEU GLY THR ILE SEQRES 6 C 165 PHE GLY THR ASP ARG PRO GLN TRP ARG GLY ALA SER GLY SEQRES 7 C 165 ALA ASP MET ILE ARG HIS VAL ARG GLY LEU VAL GLU ASN SEQRES 8 C 165 ALA GLY PHE VAL ILE GLY ASN ALA THR VAL GLN VAL ILE SEQRES 9 C 165 GLY ASN ARG PRO LYS VAL GLY PRO ARG ARG GLU GLU ALA SEQRES 10 C 165 GLN GLN VAL LEU SER GLU LEU VAL GLY ALA PRO VAL SER SEQRES 11 C 165 VAL SER ALA THR THR THR ASP GLY LEU GLY LEU THR GLY SEQRES 12 C 165 ARG GLY GLU GLY LEU ALA ALA ILE ALA THR ALA LEU VAL SEQRES 13 C 165 ALA ALA GLU PRO VAL GLY ASP ALA LYS HET ZN A1157 1 HET CDP A1158 50 HET EDO A1160 4 HET GOL A1161 6 HET ZN B1157 1 HET CDP B1158 50 HET IPE B1160 14 HET GOL B1161 6 HET PEG B1162 7 HET PEG B1163 7 HET ZN C1157 1 HET CDP C1158 50 HET EDO C1160 4 HET GOL C1161 6 HET ACT C1162 4 HETNAM ZN ZINC ION HETNAM CDP CYTIDINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM IPE 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPE ISOPENTENYL PYROPHOSPHATE FORMUL 4 ZN 3(ZN 2+) FORMUL 5 CDP 3(C9 H15 N3 O11 P2) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 10 IPE C5 H12 O7 P2 FORMUL 12 PEG 2(C4 H10 O3) FORMUL 18 ACT C2 H3 O2 1- FORMUL 19 HOH *272(H2 O) HELIX 1 1 ASP A 41 ALA A 55 1 15 HELIX 2 2 ASP A 59 GLY A 65 1 7 HELIX 3 3 ARG A 68 ARG A 72 5 5 HELIX 4 4 SER A 75 ALA A 90 1 16 HELIX 5 5 VAL A 108 PRO A 110 5 3 HELIX 6 6 ARG A 111 GLY A 124 1 14 HELIX 7 7 LEU A 137 ARG A 142 1 6 HELIX 8 8 ASP B 41 ALA B 55 1 15 HELIX 9 9 ASP B 59 GLY B 65 1 7 HELIX 10 10 ARG B 68 ARG B 72 5 5 HELIX 11 11 SER B 75 ALA B 90 1 16 HELIX 12 12 VAL B 108 PRO B 110 5 3 HELIX 13 13 ARG B 111 GLY B 124 1 14 HELIX 14 14 LEU B 137 ARG B 142 1 6 HELIX 15 15 ASP C 41 ALA C 55 1 15 HELIX 16 16 ASP C 59 GLY C 65 1 7 HELIX 17 17 ARG C 68 ARG C 72 5 5 HELIX 18 18 SER C 75 ALA C 90 1 16 HELIX 19 19 VAL C 108 PRO C 110 5 3 HELIX 20 20 ARG C 111 GLY C 124 1 14 SHEET 1 AA 4 ARG A 5 PRO A 14 0 SHEET 2 AA 4 GLY A 145 ALA A 156 -1 O LEU A 146 N HIS A 13 SHEET 3 AA 4 PHE A 92 ILE A 102 -1 O VAL A 93 N ALA A 155 SHEET 4 AA 4 VAL A 127 THR A 132 1 O SER A 128 N VAL A 99 SHEET 1 AB 2 ARG A 22 LEU A 23 0 SHEET 2 AB 2 LEU A 26 GLU A 27 -1 O LEU A 26 N LEU A 23 SHEET 1 BA 5 LEU B 26 CYS B 34 0 SHEET 2 BA 5 ARG B 5 LEU B 23 -1 N GLU B 16 O GLY B 33 SHEET 3 BA 5 GLY B 145 ALA B 156 -1 O LEU B 146 N HIS B 13 SHEET 4 BA 5 PHE B 92 ILE B 102 -1 O VAL B 93 N ALA B 155 SHEET 5 BA 5 VAL B 127 THR B 132 1 O SER B 128 N VAL B 99 SHEET 1 CA 4 ARG C 5 PRO C 14 0 SHEET 2 CA 4 GLY C 145 ALA C 156 -1 O LEU C 146 N HIS C 13 SHEET 3 CA 4 PHE C 92 ILE C 102 -1 O VAL C 93 N ALA C 155 SHEET 4 CA 4 VAL C 127 THR C 132 1 O SER C 128 N VAL C 99 SHEET 1 CB 2 CYS C 21 LEU C 23 0 SHEET 2 CB 2 LEU C 26 PHE C 28 -1 O LEU C 26 N LEU C 23 LINK OD2 ASP A 11 ZN ZN A1157 1555 1555 2.20 LINK NE2 HIS A 13 ZN ZN A1157 1555 1555 2.09 LINK ND1 HIS A 45 ZN ZN A1157 1555 1555 2.17 LINK OD1 ASP B 11 ZN ZN C1157 1555 1555 2.38 LINK NE2 HIS B 13 ZN ZN C1157 1555 1555 2.12 LINK ND1 HIS B 45 ZN ZN C1157 1555 1555 2.01 LINK ZN ZN B1157 OD2 ASP C 11 1555 1555 2.23 LINK ZN ZN B1157 NE2 HIS C 13 1555 1555 2.26 LINK ZN ZN B1157 ND1 HIS C 45 1555 1555 2.26 CISPEP 1 ASP A 32 GLY A 33 0 13.52 CISPEP 2 ARG A 105 PRO A 106 0 2.81 CISPEP 3 ARG B 105 PRO B 106 0 1.80 CISPEP 4 ASP C 32 GLY C 33 0 25.69 CISPEP 5 ARG C 105 PRO C 106 0 -2.51 SITE 1 AC1 4 ASP A 11 HIS A 13 HIS A 45 CDP C1158 SITE 1 AC2 25 GLY A 103 ASN A 104 PRO A 106 LYS A 107 SITE 2 AC2 25 VAL A 108 GLY A 109 ALA A 131 THR A 132 SITE 3 AC2 25 THR A 133 HOH A2072 HOH A2073 HOH A2074 SITE 4 AC2 25 HOH A2075 HOH A2076 HOH A2077 HOH A2078 SITE 5 AC2 25 ASP B 11 VAL B 12 HIS B 13 HIS B 45 SITE 6 AC2 25 ASP B 59 LEU B 60 GLY B 61 HOH B2037 SITE 7 AC2 25 ZN C1157 SITE 1 AC3 4 CDP B1158 ASP C 11 HIS C 13 HIS C 45 SITE 1 AC4 23 ARG B 72 GLY B 103 ASN B 104 PRO B 106 SITE 2 AC4 23 LYS B 107 VAL B 108 GLY B 109 ALA B 131 SITE 3 AC4 23 THR B 132 THR B 133 ZN B1157 HOH B2102 SITE 4 AC4 23 HOH B2103 HOH B2104 HOH B2105 HOH B2106 SITE 5 AC4 23 ASP C 11 VAL C 12 HIS C 13 ASP C 59 SITE 6 AC4 23 LEU C 60 GLY C 61 HOH C2028 SITE 1 AC5 4 CDP A1158 ASP B 11 HIS B 13 HIS B 45 SITE 1 AC6 22 ASP A 11 VAL A 12 HIS A 13 ASP A 59 SITE 2 AC6 22 GLY A 61 ZN A1157 HOH A2020 GLY C 103 SITE 3 AC6 22 ASN C 104 PRO C 106 LYS C 107 VAL C 108 SITE 4 AC6 22 GLY C 109 ALA C 131 THR C 132 THR C 133 SITE 5 AC6 22 ASP C 135 HOH C2075 HOH C2076 HOH C2078 SITE 6 AC6 22 HOH C2079 HOH C2080 SITE 1 AC7 10 SER A 53 GLY A 56 LEU A 57 GLY A 58 SITE 2 AC7 10 ARG C 112 GLN C 116 SER C 128 VAL C 129 SITE 3 AC7 10 SER C 130 HOH C2071 SITE 1 AC8 11 ARG A 112 GLN A 116 SER A 128 VAL A 129 SITE 2 AC8 11 SER A 130 HOH A2079 LEU B 52 SER B 53 SITE 3 AC8 11 GLY B 56 LEU B 57 GLY B 58 SITE 1 AC9 9 GLY A 138 LEU A 139 ARG A 142 GLY B 138 SITE 2 AC9 9 LEU B 139 ARG B 142 ALA B 147 GLY C 138 SITE 3 AC9 9 LEU C 139 SITE 1 BC1 6 GLY A 85 ASN A 89 GLY C 124 ACT C1162 SITE 2 BC1 6 HOH C2068 HOH C2081 SITE 1 BC2 6 GLN A 116 VAL A 127 SER A 128 HOH A2080 SITE 2 BC2 6 ARG B 5 HOH B2004 SITE 1 BC3 7 PRO B 14 ILE B 15 GLU B 16 GLU B 121 SITE 2 BC3 7 PEG B1162 HOH B2107 HOH B2108 SITE 1 BC4 7 HIS A 82 GLY A 85 ASN A 89 ARG C 84 SITE 2 BC4 7 GLU C 121 GLY C 124 GOL C1161 SITE 1 BC5 10 ILE B 15 CYS B 25 ALA B 77 ARG B 81 SITE 2 BC5 10 VAL B 118 ARG B 142 GLU B 144 GOL B1161 SITE 3 BC5 10 HOH B2038 HOH B2088 SITE 1 BC6 8 ARG B 19 ASP B 30 ALA B 31 ASP B 32 SITE 2 BC6 8 ARG B 81 HIS B 82 HOH B2109 ARG C 142 CRYST1 159.121 159.121 54.160 90.00 90.00 90.00 I 4 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006285 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018464 0.00000 MTRIX1 1 -0.405800 -0.384400 0.829200 76.22000 1 MTRIX2 1 0.893500 0.024160 0.448400 -12.68000 1 MTRIX3 1 -0.192400 0.922900 0.333600 -18.14000 1 MTRIX1 2 -0.381100 0.901300 -0.206200 36.96000 1 MTRIX2 2 -0.414600 0.032750 0.909400 48.24000 1 MTRIX3 2 0.826400 0.432100 0.361200 -51.23000 1 MTRIX1 3 -0.376600 -0.417900 0.826800 76.71000 1 MTRIX2 3 0.899700 0.047550 0.433800 -13.65000 1 MTRIX3 3 -0.220600 0.907200 0.358100 -16.68000 1