HEADER RECOMBINATION/REPLICATION/LIGASE 11-JUN-09 3HTK TITLE CRYSTAL STRUCTURE OF MMS21 AND SMC5 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL COIL; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 5; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: C-TERMINAL COIL; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: E3 SUMO-PROTEIN LIGASE MMS21; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: METHYL METHANESULFONATE-SENSITIVITY PROTEIN 21, NON- COMPND 15 STRUCTURAL MAINTENANCE OF CHROMOSOME ELEMENT 2, NON-SMC ELEMENT 2; COMPND 16 EC: 6.3.2.-; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SMC5, YOL034W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24D; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 GENE: SMC5, YOL034W; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET24D; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 21 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 22 ORGANISM_TAXID: 4932; SOURCE 23 GENE: MMS21, NSE2, YEL019C; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS SUMO E3 LIGASE, SPL-RING, RING, ATP-BINDING, CHROMOSOMAL PROTEIN, KEYWDS 2 COILED COIL, DNA DAMAGE, DNA RECOMBINATION, DNA REPAIR, NUCLEOTIDE- KEYWDS 3 BINDING, NUCLEUS, UBL CONJUGATION, CYTOPLASM, LIGASE, METAL-BINDING, KEYWDS 4 UBL CONJUGATION PATHWAY, ZINC, ZINC-FINGER, RECOMBINATION- KEYWDS 5 REPLICATION-LIGASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.DUAN,P.SARANGI,X.LIU,G.K.RANGI,X.ZHAO,H.YE REVDAT 2 21-FEB-24 3HTK 1 REMARK REVDAT 1 20-OCT-09 3HTK 0 JRNL AUTH X.DUAN,P.SARANGI,X.LIU,G.K.RANGI,X.ZHAO,H.YE JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE ROLES OF THE JRNL TITL 2 MMS21 SUBUNIT OF THE SMC5/6 COMPLEX. JRNL REF MOL.CELL V. 35 657 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19748359 JRNL DOI 10.1016/J.MOLCEL.2009.06.032 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 3 NUMBER OF REFLECTIONS : 20105 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) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 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) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 784 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3870 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 0.52000 REMARK 3 B33 (A**2) : -1.21000 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): 0.464 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.278 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3155 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4261 ; 1.266 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 3.674 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;45.089 ;26.424 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 612 ;14.142 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.611 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2348 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1723 ; 0.289 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2283 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 120 ; 0.155 ; 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): 32 ; 0.281 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.156 ; 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): 1946 ;12.749 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3173 ;17.317 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1209 ; 5.353 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1088 ; 8.026 ; 4.500 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 3HTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-06; 17-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : NULL; NULL REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 19-ID; 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97899; 0.97916 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 40MM CACL2, PH 7.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 124.60750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 124.60750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 23.73250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.78700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.73250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.78700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 124.60750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.73250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.78700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 124.60750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.73250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.78700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 MET C 1 REMARK 465 ALA C 2 REMARK 465 LEU C 3 REMARK 465 ASN C 4 REMARK 465 ARG C 259 REMARK 465 SER C 260 REMARK 465 SER C 261 REMARK 465 GLN C 262 REMARK 465 ALA C 263 REMARK 465 ILE C 264 REMARK 465 ASP C 265 REMARK 465 VAL C 266 REMARK 465 LEU C 267 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 LYS A 304 CG CD CE NZ REMARK 470 PRO A 305 CG CD REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 ARG A 363 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 739 CG OD1 OD2 REMARK 470 LYS C 258 CG CD CE NZ 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 SER C 55 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 PRO C 162 CB - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 GLU C 170 N - CA - C ANGL. DEV. = -17.1 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 ALA A 307 -50.98 -20.70 REMARK 500 VAL B 740 -7.51 -58.63 REMARK 500 PRO C 54 131.38 -22.93 REMARK 500 SER C 55 -170.40 -65.52 REMARK 500 THR C 56 43.41 94.88 REMARK 500 ILE C 57 10.94 -163.10 REMARK 500 ASN C 128 51.76 -100.34 REMARK 500 PRO C 130 -73.27 -37.41 REMARK 500 THR C 131 41.08 75.54 REMARK 500 THR C 136 -162.58 -121.50 REMARK 500 ASP C 156 81.38 -156.00 REMARK 500 PRO C 157 -9.45 -49.07 REMARK 500 CYS C 159 129.05 -37.92 REMARK 500 PRO C 167 -176.46 -59.50 REMARK 500 ALA C 168 -7.78 73.20 REMARK 500 ILE C 175 106.20 -58.03 REMARK 500 GLU C 176 -176.27 -68.56 REMARK 500 LEU C 182 48.06 -91.60 REMARK 500 PRO C 185 4.76 -66.96 REMARK 500 THR C 187 -24.85 -150.83 REMARK 500 TYR C 191 170.38 -52.67 REMARK 500 GLU C 192 -7.77 -160.60 REMARK 500 ALA C 193 60.26 -164.92 REMARK 500 ASN C 201 36.82 -95.40 REMARK 500 GLN C 223 109.01 -50.86 REMARK 500 ALA C 224 27.21 45.35 REMARK 500 CYS C 226 120.00 -28.92 REMARK 500 SER C 227 -48.04 -29.38 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 ILE C 57 GLY C 58 -121.33 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 ZN C 268 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 200 SG REMARK 620 2 HIS C 202 ND1 83.7 REMARK 620 3 CYS C 221 SG 99.5 92.4 REMARK 620 4 CYS C 226 SG 128.1 109.8 128.2 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 ZN C 268 DBREF 3HTK A 304 363 UNP Q08204 SMC5_YEAST 304 363 DBREF 3HTK B 739 811 UNP Q08204 SMC5_YEAST 739 811 DBREF 3HTK C 1 267 UNP P38632 NSE2_YEAST 1 267 SEQRES 1 A 60 LYS PRO PHE ALA ASN THR LYS LYS THR LEU GLU ASN GLN SEQRES 2 A 60 VAL GLU GLU LEU THR GLU LYS CYS SER LEU LYS THR ASP SEQRES 3 A 60 GLU PHE LEU LYS ALA LYS GLU LYS ILE ASN GLU ILE PHE SEQRES 4 A 60 GLU LYS LEU ASN THR ILE ARG ASP GLU VAL ILE LYS LYS SEQRES 5 A 60 LYS ASN GLN ASN GLU TYR TYR ARG SEQRES 1 B 73 ASP VAL SER GLN LYS ILE LYS ASP ILE ASP ASP GLN ILE SEQRES 2 B 73 GLN GLN LEU LEU LEU LYS GLN ARG HIS LEU LEU SER LYS SEQRES 3 B 73 MET ALA SER SER MET LYS SER LEU LYS ASN CYS GLN LYS SEQRES 4 B 73 GLU LEU ILE SER THR GLN ILE LEU GLN PHE GLU ALA GLN SEQRES 5 B 73 ASN MET ASP VAL SER MET ASN ASP VAL ILE GLY PHE PHE SEQRES 6 B 73 ASN GLU ARG GLU ALA ASP LEU LYS SEQRES 1 C 267 MET ALA LEU ASN ASP ASN PRO ILE PRO LYS SER VAL PRO SEQRES 2 C 267 LEU HIS PRO LYS SER GLY LYS TYR PHE HIS ASN LEU HIS SEQRES 3 C 267 ALA ARG ASP LEU SER ASN ILE TYR GLN GLN CYS TYR LYS SEQRES 4 C 267 GLN ILE ASP GLU THR ILE ASN GLN LEU VAL ASP SER THR SEQRES 5 C 267 SER PRO SER THR ILE GLY ILE GLU GLU GLN VAL ALA ASP SEQRES 6 C 267 ILE THR SER THR TYR LYS LEU LEU SER THR TYR GLU SER SEQRES 7 C 267 GLU SER ASN SER PHE ASP GLU HIS ILE LYS ASP LEU LYS SEQRES 8 C 267 LYS ASN PHE LYS GLN SER SER ASP ALA CYS PRO GLN ILE SEQRES 9 C 267 ASP LEU SER THR TRP ASP LYS TYR ARG THR GLY GLU LEU SEQRES 10 C 267 THR ALA PRO LYS LEU SER GLU LEU TYR LEU ASN MET PRO SEQRES 11 C 267 THR PRO GLU PRO ALA THR MET VAL ASN ASN THR ASP THR SEQRES 12 C 267 LEU LYS ILE LEU LYS VAL LEU PRO TYR ILE TRP ASN ASP SEQRES 13 C 267 PRO THR CYS VAL ILE PRO ASP LEU GLN ASN PRO ALA ASP SEQRES 14 C 267 GLU ASP ASP LEU GLN ILE GLU GLY GLY LYS ILE GLU LEU SEQRES 15 C 267 THR CYS PRO ILE THR CYS LYS PRO TYR GLU ALA PRO LEU SEQRES 16 C 267 ILE SER ARG LYS CYS ASN HIS VAL PHE ASP ARG ASP GLY SEQRES 17 C 267 ILE GLN ASN TYR LEU GLN GLY TYR THR THR ARG ASP CYS SEQRES 18 C 267 PRO GLN ALA ALA CYS SER GLN VAL VAL SER MET ARG ASP SEQRES 19 C 267 PHE VAL ARG ASP PRO ILE MET GLU LEU ARG CYS LYS ILE SEQRES 20 C 267 ALA LYS MET LYS GLU SER GLN GLU GLN ASP LYS ARG SER SEQRES 21 C 267 SER GLN ALA ILE ASP VAL LEU HET ZN C 268 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *117(H2 O) HELIX 1 1 PHE A 306 TYR A 361 1 56 HELIX 2 2 GLN B 742 ASP B 809 1 68 HELIX 3 3 HIS C 15 LYS C 17 5 3 HELIX 4 4 SER C 18 LEU C 25 1 8 HELIX 5 5 LEU C 30 THR C 52 1 23 HELIX 6 6 ILE C 59 ALA C 100 1 42 HELIX 7 7 SER C 107 GLY C 115 1 9 HELIX 8 8 LYS C 121 ASN C 128 1 8 HELIX 9 9 THR C 141 ASP C 156 1 16 HELIX 10 10 ARG C 206 LEU C 213 1 8 HELIX 11 11 PRO C 222 CYS C 226 5 5 HELIX 12 12 SER C 231 ARG C 233 5 3 HELIX 13 13 ASP C 238 ASP C 257 1 20 SHEET 1 A 3 VAL C 203 ASP C 205 0 SHEET 2 A 3 PRO C 194 SER C 197 -1 N LEU C 195 O PHE C 204 SHEET 3 A 3 PHE C 235 ARG C 237 -1 O VAL C 236 N ILE C 196 SHEET 1 B 2 ARG C 219 ASP C 220 0 SHEET 2 B 2 VAL C 229 VAL C 230 -1 O VAL C 230 N ARG C 219 LINK SG CYS C 200 ZN ZN C 268 1555 1555 2.59 LINK ND1 HIS C 202 ZN ZN C 268 1555 1555 2.13 LINK SG CYS C 221 ZN ZN C 268 1555 1555 2.60 LINK SG CYS C 226 ZN ZN C 268 1555 1555 2.72 CISPEP 1 GLU C 133 PRO C 134 0 0.05 SITE 1 AC1 4 CYS C 200 HIS C 202 CYS C 221 CYS C 226 CRYST1 47.465 91.574 249.215 90.00 90.00 90.00 C 2 2 21 8 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 0.021068 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004013 0.00000