PDB Short entry for 3DC5 HEADER OXIDOREDUCTASE 03-JUN-08 3DC5 TITLE CRYSTAL STRUCTURE OF A MANGANESE SUPEROXIDE DISMUTASES FROM TITLE 2 CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [MN] 2; 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-3, C08A9.1; 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 3 01-NOV-23 3DC5 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3DC5 1 VERSN REVDAT 1 09-JUN-09 3DC5 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 49346 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2502 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3348 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 420 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.13000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.923 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3230 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4377 ; 1.398 ; 1.928 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 387 ; 4.430 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;30.043 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 553 ;11.321 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;11.874 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2478 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1646 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2219 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 332 ; 0.121 ; 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): 61 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.081 ; 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): 2014 ; 0.855 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3102 ; 1.149 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1440 ; 2.022 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1275 ; 3.029 ; 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 194 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7870 5.9450 -0.8920 REMARK 3 T TENSOR REMARK 3 T11: -0.0266 T22: -0.0706 REMARK 3 T33: 0.1460 T12: 0.0261 REMARK 3 T13: 0.0351 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.3733 L22: 1.7851 REMARK 3 L33: 1.4371 L12: 0.1860 REMARK 3 L13: 0.0404 L23: -0.7409 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: -0.0416 S13: -0.1054 REMARK 3 S21: -0.1452 S22: -0.1550 S23: -0.3853 REMARK 3 S31: 0.2663 S32: 0.1384 S33: 0.1541 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 194 REMARK 3 ORIGIN FOR THE GROUP (A): -8.7530 -2.5360 14.1280 REMARK 3 T TENSOR REMARK 3 T11: -0.0634 T22: -0.0166 REMARK 3 T33: 0.1348 T12: 0.0006 REMARK 3 T13: 0.0675 T23: 0.0609 REMARK 3 L TENSOR REMARK 3 L11: 1.3820 L22: 1.2766 REMARK 3 L33: 0.8784 L12: -0.1126 REMARK 3 L13: 0.1410 L23: -0.3000 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.2551 S13: -0.0911 REMARK 3 S21: 0.1849 S22: 0.0616 S23: 0.3050 REMARK 3 S31: -0.0412 S32: -0.1624 S33: -0.0844 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 3DC5 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_1000047853. 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 : 49346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : 0.36400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1N0J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.7M 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 68.01550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.89000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.00775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.89000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.89000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.02325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.89000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.89000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.00775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.89000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.89000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.02325 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 68.01550 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: 7930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.2 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 199 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 197 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 1 CG CD CE NZ REMARK 470 LYS A 90 CG CD CE NZ 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 -120.17 53.13 REMARK 500 TYR A 161 -12.47 -145.45 REMARK 500 LYS A 166 -130.39 51.12 REMARK 500 ASN C 141 -120.41 49.73 REMARK 500 TYR C 161 -18.03 -147.81 REMARK 500 LYS C 166 -134.16 51.17 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 195 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 74 NE2 97.6 REMARK 620 3 ASP A 155 OD1 82.8 112.7 REMARK 620 4 HIS A 159 NE2 90.7 124.6 122.7 REMARK 620 5 HOH A 197 O 171.0 89.8 89.7 89.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 195 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 26 NE2 REMARK 620 2 HIS C 74 NE2 95.4 REMARK 620 3 ASP C 155 OD1 85.0 109.1 REMARK 620 4 HIS C 159 NE2 89.3 131.9 119.0 REMARK 620 5 HOH C 196 O 168.3 92.2 84.1 92.2 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 C 195 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 195 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 196 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DC6 RELATED DB: PDB DBREF 3DC5 A 1 194 UNP P41977 SODM2_CAEEL 25 218 DBREF 3DC5 C 1 194 UNP P41977 SODM2_CAEEL 25 218 SEQADV 3DC5 MET A 0 UNP P41977 INITIATING METHIONINE SEQADV 3DC5 MET C 0 UNP P41977 INITIATING METHIONINE SEQRES 1 A 195 MET LYS HIS THR LEU PRO ASP LEU PRO PHE ASP TYR ALA SEQRES 2 A 195 ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU SEQRES 3 A 195 HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU SEQRES 4 A 195 ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS SEQRES 5 A 195 GLY ASN LEU LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU SEQRES 6 A 195 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 A 195 TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER LYS SEQRES 8 A 195 GLU LEU MET ASP THR ILE LYS ARG ASP PHE GLY SER LEU SEQRES 9 A 195 ASP ASN LEU GLN LYS ARG LEU SER ASP ILE THR ILE ALA SEQRES 10 A 195 VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS LYS SEQRES 11 A 195 LYS ASP LYS ILE LEU LYS ILE ALA THR CYS ALA ASN GLN SEQRES 12 A 195 ASP PRO LEU GLU GLY MET VAL PRO LEU PHE GLY ILE ASP SEQRES 13 A 195 VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR LYS ASN VAL SEQRES 14 A 195 ARG PRO ASP TYR VAL HIS ALA ILE TRP LYS ILE ALA ASN SEQRES 15 A 195 TRP LYS ASN ILE SER GLU ARG PHE ALA ASN ALA ARG GLN SEQRES 1 C 195 MET LYS HIS THR LEU PRO ASP LEU PRO PHE ASP TYR ALA SEQRES 2 C 195 ASP LEU GLU PRO VAL ILE SER HIS GLU ILE MET GLN LEU SEQRES 3 C 195 HIS HIS GLN LYS HIS HIS ALA THR TYR VAL ASN ASN LEU SEQRES 4 C 195 ASN GLN ILE GLU GLU LYS LEU HIS GLU ALA VAL SER LYS SEQRES 5 C 195 GLY ASN LEU LYS GLU ALA ILE ALA LEU GLN PRO ALA LEU SEQRES 6 C 195 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 C 195 TRP THR ASN LEU ALA LYS ASP GLY GLY GLU PRO SER LYS SEQRES 8 C 195 GLU LEU MET ASP THR ILE LYS ARG ASP PHE GLY SER LEU SEQRES 9 C 195 ASP ASN LEU GLN LYS ARG LEU SER ASP ILE THR ILE ALA SEQRES 10 C 195 VAL GLN GLY SER GLY TRP GLY TRP LEU GLY TYR CYS LYS SEQRES 11 C 195 LYS ASP LYS ILE LEU LYS ILE ALA THR CYS ALA ASN GLN SEQRES 12 C 195 ASP PRO LEU GLU GLY MET VAL PRO LEU PHE GLY ILE ASP SEQRES 13 C 195 VAL TRP GLU HIS ALA TYR TYR LEU GLN TYR LYS ASN VAL SEQRES 14 C 195 ARG PRO ASP TYR VAL HIS ALA ILE TRP LYS ILE ALA ASN SEQRES 15 C 195 TRP LYS ASN ILE SER GLU ARG PHE ALA ASN ALA ARG GLN HET MN A 195 1 HET MLI A 196 7 HET MN C 195 1 HETNAM MN MANGANESE (II) ION HETNAM MLI MALONATE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 MLI C3 H2 O4 2- FORMUL 6 HOH *420(H2 O) HELIX 1 1 SER A 19 LYS A 29 1 11 HELIX 2 2 LYS A 29 GLY A 52 1 24 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 TRP A 157 ALA A 160 5 4 HELIX 8 8 TYR A 161 LYS A 166 1 6 HELIX 9 9 VAL A 168 TRP A 177 1 10 HELIX 10 10 LYS A 178 ALA A 180 5 3 HELIX 11 11 ASN A 181 GLN A 194 1 14 HELIX 12 12 SER C 19 LYS C 29 1 11 HELIX 13 13 LYS C 29 GLY C 52 1 24 HELIX 14 14 ASN C 53 LEU C 60 1 8 HELIX 15 15 LEU C 60 ASN C 80 1 21 HELIX 16 16 SER C 89 GLY C 101 1 13 HELIX 17 17 SER C 102 ALA C 116 1 15 HELIX 18 18 TRP C 157 ALA C 160 5 4 HELIX 19 19 TYR C 161 LYS C 166 1 6 HELIX 20 20 VAL C 168 TRP C 177 1 10 HELIX 21 21 LYS C 178 ALA C 180 5 3 HELIX 22 22 ASN C 181 ARG C 193 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 TRP A 124 O ALA A 137 SHEET 3 A 3 VAL A 149 ASP A 155 -1 O VAL A 149 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 GLY C 126 O LYS C 135 SHEET 3 B 3 VAL C 149 ASP C 155 -1 O LEU C 151 N LEU C 125 LINK NE2 HIS A 26 MN MN A 195 1555 1555 2.24 LINK NE2 HIS A 74 MN MN A 195 1555 1555 2.18 LINK OD1 ASP A 155 MN MN A 195 1555 1555 2.05 LINK NE2 HIS A 159 MN MN A 195 1555 1555 2.23 LINK MN MN A 195 O HOH A 197 1555 1555 2.25 LINK NE2 HIS C 26 MN MN C 195 1555 1555 2.22 LINK NE2 HIS C 74 MN MN C 195 1555 1555 2.19 LINK OD1 ASP C 155 MN MN C 195 1555 1555 2.07 LINK NE2 HIS C 159 MN MN C 195 1555 1555 2.13 LINK MN MN C 195 O HOH C 196 1555 1555 2.26 CISPEP 1 GLU A 15 PRO A 16 0 2.67 CISPEP 2 GLU C 15 PRO C 16 0 2.87 SITE 1 AC1 4 HIS C 26 HIS C 74 ASP C 155 HIS C 159 SITE 1 AC2 4 HIS A 26 HIS A 74 ASP A 155 HIS A 159 SITE 1 AC3 1 ASN A 167 CRYST1 81.780 81.780 136.031 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 0.012228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007351 0.00000