PDB Short entry for 3DC6 HEADER OXIDOREDUCTASE 03-JUN-08 3DC6 TITLE CRYSTAL STRUCTURE OF A MANGANESE SUPEROXIDE DISMUTASES FROM TITLE 2 CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [MN] 1; COMPND 3 CHAIN: A, C; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: SOD-2, SDM-1, F10D11.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: OX326A; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRC-99A KEYWDS ALPHA HAIRPIN N DOMAIN, ALPHA/BETA C DOMAIN, OXIDOREDUCTASE, KEYWDS 2 MANGANESE, METAL-BINDING, MITOCHONDRION, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR C.H.TRINH,T.HUNTER,E.E.STEWART,S.E.V.PHILLIPS,G.J.HUNTER REVDAT 4 03-APR-24 3DC6 1 REMARK REVDAT 3 20-MAR-24 3DC6 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3DC6 1 VERSN REVDAT 1 09-JUN-09 3DC6 0 JRNL AUTH C.H.TRINH,T.HUNTER,E.E.STEWART,S.E.PHILLIPS,G.J.HUNTER JRNL TITL PURIFICATION, CRYSTALLIZATION AND X-RAY STRUCTURES OF THE JRNL TITL 2 TWO MANGANESE SUPEROXIDE DISMUTASES FROM CAENORHABDITIS JRNL TITL 3 ELEGANS JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 64 1110 2008 JRNL REFN ESSN 1744-3091 JRNL PMID 19052361 JRNL DOI 10.1107/S1744309108037056 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 41573 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2105 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2935 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 159 REMARK 3 BIN FREE R VALUE : 0.2080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3105 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 448 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.31000 REMARK 3 B33 (A**2) : 0.61000 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): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.773 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3276 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4471 ; 1.109 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 410 ; 5.054 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;33.408 ;25.686 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;11.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ; 4.469 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 480 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2522 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1697 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2260 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 376 ; 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): 59 ; 0.138 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.200 ; 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): 2075 ; 0.605 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3224 ; 0.837 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1414 ; 1.472 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1244 ; 2.317 ; 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 : 2 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 197 REMARK 3 ORIGIN FOR THE GROUP (A): 26.1720 5.3940 -0.9700 REMARK 3 T TENSOR REMARK 3 T11: 0.0490 T22: 0.0176 REMARK 3 T33: -0.0115 T12: 0.0166 REMARK 3 T13: 0.0023 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.5920 L22: 0.6931 REMARK 3 L33: 1.1730 L12: 0.1245 REMARK 3 L13: -0.3005 L23: -0.4522 REMARK 3 S TENSOR REMARK 3 S11: -0.0452 S12: 0.0267 S13: -0.0616 REMARK 3 S21: -0.0464 S22: -0.0066 S23: -0.1059 REMARK 3 S31: 0.1675 S32: 0.0831 S33: 0.0518 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 : C 0 C 197 REMARK 3 ORIGIN FOR THE GROUP (A): -8.5080 -3.5180 14.3350 REMARK 3 T TENSOR REMARK 3 T11: -0.0016 T22: 0.2685 REMARK 3 T33: -0.0452 T12: 0.0691 REMARK 3 T13: 0.0393 T23: 0.1226 REMARK 3 L TENSOR REMARK 3 L11: 2.5660 L22: 1.4318 REMARK 3 L33: 3.1288 L12: -0.8458 REMARK 3 L13: 1.7219 L23: -1.4417 REMARK 3 S TENSOR REMARK 3 S11: -0.1147 S12: -0.7337 S13: -0.1566 REMARK 3 S21: 0.1666 S22: 0.5027 S23: 0.3467 REMARK 3 S31: -0.1798 S32: -1.0738 S33: -0.3879 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 3DC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.060 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : 41573 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 69.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.14400 REMARK 200 R SYM FOR SHELL (I) : 0.14400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: C. ELEGANS MNSOD3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3M AMMONIUM SULPHATE, 0.1M BICINE, REMARK 280 PH9.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 68.72200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.49000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.36100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.49000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.49000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.08300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.49000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.49000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.36100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.49000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.49000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 103.08300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.72200 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 200 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 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 LYS A 130 CG CD CE NZ REMARK 470 LYS C 83 CG CD CE NZ REMARK 470 ASP C 84 CG OD1 OD2 REMARK 470 GLU C 87 CG CD OE1 OE2 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 141 -125.30 52.23 REMARK 500 TYR A 164 -12.33 -149.39 REMARK 500 LYS A 169 -133.01 53.60 REMARK 500 ASN C 141 -124.97 51.09 REMARK 500 TYR C 164 -11.37 -149.05 REMARK 500 LYS C 169 -132.29 52.55 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 MN A 198 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 74 NE2 90.1 REMARK 620 3 ASP A 158 OD1 84.8 113.9 REMARK 620 4 HIS A 162 NE2 90.5 128.7 117.2 REMARK 620 5 HOH A 202 O 176.6 92.4 92.2 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 198 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 26 NE2 REMARK 620 2 HIS C 74 NE2 88.9 REMARK 620 3 ASP C 158 OD1 84.2 112.3 REMARK 620 4 HIS C 162 NE2 89.6 125.6 121.6 REMARK 620 5 HOH C 220 O 173.7 93.3 89.5 94.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 199 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DC5 RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN DBREF 3DC6 A 1 197 UNP P31161 SODM1_CAEEL 25 221 DBREF 3DC6 C 1 197 UNP P31161 SODM1_CAEEL 25 221 SEQADV 3DC6 MET A 0 UNP P31161 INITIATING METHIONINE SEQADV 3DC6 MET C 0 UNP P31161 INITIATING METHIONINE SEQRES 1 A 198 MET LYS HIS SER LEU PRO ASP LEU PRO TYR ASP TYR ALA SEQRES 2 A 198 ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU SEQRES 3 A 198 HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU SEQRES 4 A 198 ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS SEQRES 5 A 198 GLY ASN VAL LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU SEQRES 6 A 198 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 A 198 TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER ALA SEQRES 8 A 198 GLU LEU LEU THR ALA ILE LYS SER ASP PHE GLY SER LEU SEQRES 9 A 198 ASP ASN LEU GLN LYS GLN LEU SER ALA SER THR VAL ALA SEQRES 10 A 198 VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS PRO SEQRES 11 A 198 LYS GLY LYS ILE LEU LYS VAL ALA THR CYS ALA ASN GLN SEQRES 12 A 198 ASP PRO LEU GLU ALA THR THR GLY LEU VAL PRO LEU PHE SEQRES 13 A 198 GLY ILE ASP VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR SEQRES 14 A 198 LYS ASN VAL ARG PRO ASP TYR VAL ASN ALA ILE TRP LYS SEQRES 15 A 198 ILE ALA ASN TRP LYS ASN VAL SER GLU ARG PHE ALA LYS SEQRES 16 A 198 ALA GLN GLN SEQRES 1 C 198 MET LYS HIS SER LEU PRO ASP LEU PRO TYR ASP TYR ALA SEQRES 2 C 198 ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU SEQRES 3 C 198 HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU SEQRES 4 C 198 ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS SEQRES 5 C 198 GLY ASN VAL LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU SEQRES 6 C 198 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 C 198 TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER ALA SEQRES 8 C 198 GLU LEU LEU THR ALA ILE LYS SER ASP PHE GLY SER LEU SEQRES 9 C 198 ASP ASN LEU GLN LYS GLN LEU SER ALA SER THR VAL ALA SEQRES 10 C 198 VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS PRO SEQRES 11 C 198 LYS GLY LYS ILE LEU LYS VAL ALA THR CYS ALA ASN GLN SEQRES 12 C 198 ASP PRO LEU GLU ALA THR THR GLY LEU VAL PRO LEU PHE SEQRES 13 C 198 GLY ILE ASP VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR SEQRES 14 C 198 LYS ASN VAL ARG PRO ASP TYR VAL ASN ALA ILE TRP LYS SEQRES 15 C 198 ILE ALA ASN TRP LYS ASN VAL SER GLU ARG PHE ALA LYS SEQRES 16 C 198 ALA GLN GLN HET MN A 198 1 HET SO4 A 199 5 HET SO4 A 200 5 HET MN C 198 1 HET SO4 C 199 5 HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 SO4 3(O4 S 2-) FORMUL 8 HOH *448(H2 O) HELIX 1 1 SER A 19 LYS A 29 1 11 HELIX 2 2 LYS A 29 LYS A 51 1 23 HELIX 3 3 ASN A 53 LEU A 60 1 8 HELIX 4 4 LEU A 60 ASN A 80 1 21 HELIX 5 5 SER A 89 GLY A 101 1 13 HELIX 6 6 SER A 102 ALA A 116 1 15 HELIX 7 7 PRO A 144 GLY A 150 1 7 HELIX 8 8 TRP A 160 ALA A 163 5 4 HELIX 9 9 TYR A 164 LYS A 169 1 6 HELIX 10 10 VAL A 171 ILE A 179 1 9 HELIX 11 11 TRP A 180 ALA A 183 5 4 HELIX 12 12 ASN A 184 GLN A 196 1 13 HELIX 13 13 SER C 19 LYS C 29 1 11 HELIX 14 14 LYS C 29 GLY C 52 1 24 HELIX 15 15 ASN C 53 LEU C 60 1 8 HELIX 16 16 LEU C 60 ASN C 80 1 21 HELIX 17 17 SER C 89 GLY C 101 1 13 HELIX 18 18 SER C 102 ALA C 116 1 15 HELIX 19 19 PRO C 144 GLY C 150 1 7 HELIX 20 20 TRP C 160 ALA C 163 5 4 HELIX 21 21 TYR C 164 LYS C 169 1 6 HELIX 22 22 VAL C 171 ILE C 179 1 9 HELIX 23 23 TRP C 180 ALA C 183 5 4 HELIX 24 24 ASN C 184 GLN C 196 1 13 SHEET 1 A 3 ILE A 133 ALA A 140 0 SHEET 2 A 3 GLY A 121 CYS A 128 -1 N GLY A 126 O LYS A 135 SHEET 3 A 3 VAL A 152 ASP A 158 -1 O VAL A 152 N TYR A 127 SHEET 1 B 3 ILE C 133 ALA C 140 0 SHEET 2 B 3 GLY C 121 CYS C 128 -1 N TRP C 124 O ALA C 137 SHEET 3 B 3 VAL C 152 ASP C 158 -1 O VAL C 152 N TYR C 127 LINK NE2 HIS A 26 MN MN A 198 1555 1555 2.15 LINK NE2 HIS A 74 MN MN A 198 1555 1555 2.16 LINK OD1 ASP A 158 MN MN A 198 1555 1555 2.01 LINK NE2 HIS A 162 MN MN A 198 1555 1555 2.19 LINK MN MN A 198 O HOH A 202 1555 1555 1.95 LINK NE2 HIS C 26 MN MN C 198 1555 1555 2.22 LINK NE2 HIS C 74 MN MN C 198 1555 1555 2.15 LINK OD1 ASP C 158 MN MN C 198 1555 1555 1.99 LINK NE2 HIS C 162 MN MN C 198 1555 1555 2.17 LINK MN MN C 198 O HOH C 220 1555 1555 2.10 CISPEP 1 GLU A 15 PRO A 16 0 4.26 CISPEP 2 GLU C 15 PRO C 16 0 9.14 SITE 1 AC1 5 HIS A 26 HIS A 74 ASP A 158 HIS A 162 SITE 2 AC1 5 HOH A 202 SITE 1 AC2 6 TYR A 11 GLN A 24 GLN A 28 HOH A 323 SITE 2 AC2 6 LYS C 1 SER C 3 SITE 1 AC3 5 HIS A 2 SER A 3 HIS A 71 HOH A 288 SITE 2 AC3 5 HOH A 419 SITE 1 AC4 5 HIS C 26 HIS C 74 ASP C 158 HIS C 162 SITE 2 AC4 5 HOH C 220 SITE 1 AC5 7 HIS C 2 SER C 3 HIS C 71 HOH C 262 SITE 2 AC5 7 HOH C 318 HOH C 321 HOH C 334 CRYST1 80.980 80.980 137.444 90.00 90.00 90.00 P 41 21 2 16 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 0.012349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007276 0.00000