HEADER OXIDOREDUCTASE 30-JUN-10 3AK2 TITLE SUPEROXIDE DISMUTASE FROM AEROPYRUM PERNIX K1, MN-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [MN/FE]; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: APE0741; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS SUPEROXIDE DISMUTASE, CAMBIALISTIC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,K.UEGAKI REVDAT 3 01-NOV-23 3AK2 1 REMARK LINK REVDAT 2 23-FEB-11 3AK2 1 JRNL REVDAT 1 02-FEB-11 3AK2 0 JRNL AUTH T.NAKAMURA,K.TORIKAI,K.UEGAKI,J.MORITA,K.MACHIDA,A.SUZUKI, JRNL AUTH 2 Y.KAWATA JRNL TITL CRYSTAL STRUCTURE OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE JRNL TITL 2 FROM AEROPYRUM PERNIX K1 - INSIGHTS INTO THE ENZYME JRNL TITL 3 MECHANISM AND STABILITY JRNL REF FEBS J. V. 278 598 2011 JRNL REFN ISSN 1742-464X JRNL PMID 21182595 JRNL DOI 10.1111/J.1742-4658.2010.07977.X REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 152991 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8101 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 594 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6823 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 734 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.065 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.861 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7081 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9575 ; 1.052 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 835 ; 5.927 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 343 ;35.790 ;24.315 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1173 ;10.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.129 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 993 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5417 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3811 ; 0.186 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4864 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 680 ; 0.116 ; 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): 37 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 48 ; 0.100 ; 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): 4311 ; 0.598 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6714 ; 0.672 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3252 ; 1.144 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2861 ; 1.778 ; 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 3AK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000029348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-10 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 161154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 3AK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 8% PEG 6000, 8% ETHYLENE REMARK 280 GLYCOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.89100 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 LEU A 212 REMARK 465 PRO A 213 REMARK 465 GLN A 214 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 SER B 3 REMARK 465 PHE B 4 REMARK 465 GLN B 214 REMARK 465 LEU C 211 REMARK 465 LEU C 212 REMARK 465 PRO C 213 REMARK 465 GLN C 214 REMARK 465 MET D 1 REMARK 465 LEU D 211 REMARK 465 LEU D 212 REMARK 465 PRO D 213 REMARK 465 GLN D 214 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 O LYS D 49 O HOH D 416 1.84 REMARK 500 O HOH C 255 O HOH C 592 2.07 REMARK 500 O HOH A 248 O HOH C 541 2.19 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 LYS A 34 -61.21 -101.56 REMARK 500 LYS A 149 -126.93 47.10 REMARK 500 ASN A 151 30.89 -148.23 REMARK 500 LEU A 153 -13.66 80.79 REMARK 500 TYR A 171 -17.84 -145.18 REMARK 500 LYS A 176 -133.34 53.81 REMARK 500 LYS B 34 -64.09 -104.88 REMARK 500 LYS B 149 -129.63 50.94 REMARK 500 ASN B 151 30.38 -147.42 REMARK 500 LEU B 153 -14.06 81.93 REMARK 500 TYR B 171 -17.69 -145.67 REMARK 500 LYS B 176 -135.51 54.75 REMARK 500 LYS C 34 -62.19 -98.60 REMARK 500 LYS C 149 -125.78 47.73 REMARK 500 ASN C 151 31.66 -145.72 REMARK 500 LEU C 153 -12.64 81.35 REMARK 500 TYR C 171 -17.33 -145.58 REMARK 500 LYS C 176 -132.83 54.49 REMARK 500 LYS D 34 -62.57 -100.56 REMARK 500 LYS D 149 -126.82 51.14 REMARK 500 ASN D 151 30.36 -147.77 REMARK 500 LEU D 153 -14.30 80.90 REMARK 500 TYR D 171 -17.38 -143.95 REMARK 500 LYS D 176 -134.11 55.52 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 215 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 31 NE2 REMARK 620 2 HIS A 79 NE2 90.7 REMARK 620 3 ASP A 165 OD2 82.8 106.6 REMARK 620 4 HIS A 169 NE2 89.6 135.1 117.9 REMARK 620 5 HOH A 223 O 171.3 92.4 88.5 93.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 215 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 31 NE2 REMARK 620 2 HIS B 79 NE2 90.7 REMARK 620 3 ASP B 165 OD2 82.1 105.2 REMARK 620 4 HIS B 169 NE2 89.8 136.0 118.4 REMARK 620 5 HOH B 221 O 169.0 94.6 87.2 93.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 215 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 31 NE2 REMARK 620 2 HIS C 79 NE2 90.4 REMARK 620 3 ASP C 165 OD2 82.4 104.6 REMARK 620 4 HIS C 169 NE2 91.7 137.0 118.2 REMARK 620 5 HOH C 220 O 168.7 94.0 86.4 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 215 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 31 NE2 REMARK 620 2 HIS D 79 NE2 89.8 REMARK 620 3 ASP D 165 OD2 83.1 103.4 REMARK 620 4 HIS D 169 NE2 90.6 136.5 119.8 REMARK 620 5 HOH D 221 O 171.2 92.1 88.1 93.9 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 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN D 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 220 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AK1 RELATED DB: PDB REMARK 900 SAME PROTEIN, APO-FORM REMARK 900 RELATED ID: 3AK3 RELATED DB: PDB REMARK 900 SAME PROTEIN, FE-BOUND FORM DBREF 3AK2 A 1 214 UNP Q9Y8H8 SODF_AERPE 1 214 DBREF 3AK2 B 1 214 UNP Q9Y8H8 SODF_AERPE 1 214 DBREF 3AK2 C 1 214 UNP Q9Y8H8 SODF_AERPE 1 214 DBREF 3AK2 D 1 214 UNP Q9Y8H8 SODF_AERPE 1 214 SEQRES 1 A 214 MET VAL SER PHE LYS ARG TYR GLU LEU PRO PRO LEU PRO SEQRES 2 A 214 TYR ASN TYR ASN ALA LEU GLU PRO TYR ILE ILE GLU GLU SEQRES 3 A 214 ILE MET LYS LEU HIS HIS GLN LYS HIS HIS ASN THR TYR SEQRES 4 A 214 VAL LYS GLY ALA ASN ALA ALA LEU GLU LYS ILE GLU LYS SEQRES 5 A 214 HIS LEU LYS GLY GLU ILE GLN ILE ASP VAL ARG ALA VAL SEQRES 6 A 214 MET ARG ASP PHE SER PHE ASN TYR ALA GLY HIS ILE MET SEQRES 7 A 214 HIS THR ILE PHE TRP PRO ASN MET ALA PRO PRO GLY LYS SEQRES 8 A 214 GLY GLY GLY THR PRO GLY GLY ARG VAL ALA ASP LEU ILE SEQRES 9 A 214 GLU LYS GLN PHE GLY GLY PHE GLU LYS PHE LYS ALA LEU SEQRES 10 A 214 PHE SER ALA ALA ALA LYS THR VAL GLU GLY VAL GLY TRP SEQRES 11 A 214 GLY VAL LEU ALA PHE ASP PRO LEU THR GLU GLU LEU ARG SEQRES 12 A 214 ILE LEU GLN VAL GLU LYS HIS ASN VAL LEU MET THR ALA SEQRES 13 A 214 GLY LEU VAL PRO ILE LEU VAL ILE ASP VAL TRP GLU HIS SEQRES 14 A 214 ALA TYR TYR LEU GLN TYR LYS ASN ASP ARG GLY SER TYR SEQRES 15 A 214 VAL GLU ASN TRP TRP ASN VAL VAL ASN TRP ASP ASP VAL SEQRES 16 A 214 GLU LYS ARG LEU GLU GLN ALA LEU ASN ASN ALA LYS PRO SEQRES 17 A 214 LEU TYR LEU LEU PRO GLN SEQRES 1 B 214 MET VAL SER PHE LYS ARG TYR GLU LEU PRO PRO LEU PRO SEQRES 2 B 214 TYR ASN TYR ASN ALA LEU GLU PRO TYR ILE ILE GLU GLU SEQRES 3 B 214 ILE MET LYS LEU HIS HIS GLN LYS HIS HIS ASN THR TYR SEQRES 4 B 214 VAL LYS GLY ALA ASN ALA ALA LEU GLU LYS ILE GLU LYS SEQRES 5 B 214 HIS LEU LYS GLY GLU ILE GLN ILE ASP VAL ARG ALA VAL SEQRES 6 B 214 MET ARG ASP PHE SER PHE ASN TYR ALA GLY HIS ILE MET SEQRES 7 B 214 HIS THR ILE PHE TRP PRO ASN MET ALA PRO PRO GLY LYS SEQRES 8 B 214 GLY GLY GLY THR PRO GLY GLY ARG VAL ALA ASP LEU ILE SEQRES 9 B 214 GLU LYS GLN PHE GLY GLY PHE GLU LYS PHE LYS ALA LEU SEQRES 10 B 214 PHE SER ALA ALA ALA LYS THR VAL GLU GLY VAL GLY TRP SEQRES 11 B 214 GLY VAL LEU ALA PHE ASP PRO LEU THR GLU GLU LEU ARG SEQRES 12 B 214 ILE LEU GLN VAL GLU LYS HIS ASN VAL LEU MET THR ALA SEQRES 13 B 214 GLY LEU VAL PRO ILE LEU VAL ILE ASP VAL TRP GLU HIS SEQRES 14 B 214 ALA TYR TYR LEU GLN TYR LYS ASN ASP ARG GLY SER TYR SEQRES 15 B 214 VAL GLU ASN TRP TRP ASN VAL VAL ASN TRP ASP ASP VAL SEQRES 16 B 214 GLU LYS ARG LEU GLU GLN ALA LEU ASN ASN ALA LYS PRO SEQRES 17 B 214 LEU TYR LEU LEU PRO GLN SEQRES 1 C 214 MET VAL SER PHE LYS ARG TYR GLU LEU PRO PRO LEU PRO SEQRES 2 C 214 TYR ASN TYR ASN ALA LEU GLU PRO TYR ILE ILE GLU GLU SEQRES 3 C 214 ILE MET LYS LEU HIS HIS GLN LYS HIS HIS ASN THR TYR SEQRES 4 C 214 VAL LYS GLY ALA ASN ALA ALA LEU GLU LYS ILE GLU LYS SEQRES 5 C 214 HIS LEU LYS GLY GLU ILE GLN ILE ASP VAL ARG ALA VAL SEQRES 6 C 214 MET ARG ASP PHE SER PHE ASN TYR ALA GLY HIS ILE MET SEQRES 7 C 214 HIS THR ILE PHE TRP PRO ASN MET ALA PRO PRO GLY LYS SEQRES 8 C 214 GLY GLY GLY THR PRO GLY GLY ARG VAL ALA ASP LEU ILE SEQRES 9 C 214 GLU LYS GLN PHE GLY GLY PHE GLU LYS PHE LYS ALA LEU SEQRES 10 C 214 PHE SER ALA ALA ALA LYS THR VAL GLU GLY VAL GLY TRP SEQRES 11 C 214 GLY VAL LEU ALA PHE ASP PRO LEU THR GLU GLU LEU ARG SEQRES 12 C 214 ILE LEU GLN VAL GLU LYS HIS ASN VAL LEU MET THR ALA SEQRES 13 C 214 GLY LEU VAL PRO ILE LEU VAL ILE ASP VAL TRP GLU HIS SEQRES 14 C 214 ALA TYR TYR LEU GLN TYR LYS ASN ASP ARG GLY SER TYR SEQRES 15 C 214 VAL GLU ASN TRP TRP ASN VAL VAL ASN TRP ASP ASP VAL SEQRES 16 C 214 GLU LYS ARG LEU GLU GLN ALA LEU ASN ASN ALA LYS PRO SEQRES 17 C 214 LEU TYR LEU LEU PRO GLN SEQRES 1 D 214 MET VAL SER PHE LYS ARG TYR GLU LEU PRO PRO LEU PRO SEQRES 2 D 214 TYR ASN TYR ASN ALA LEU GLU PRO TYR ILE ILE GLU GLU SEQRES 3 D 214 ILE MET LYS LEU HIS HIS GLN LYS HIS HIS ASN THR TYR SEQRES 4 D 214 VAL LYS GLY ALA ASN ALA ALA LEU GLU LYS ILE GLU LYS SEQRES 5 D 214 HIS LEU LYS GLY GLU ILE GLN ILE ASP VAL ARG ALA VAL SEQRES 6 D 214 MET ARG ASP PHE SER PHE ASN TYR ALA GLY HIS ILE MET SEQRES 7 D 214 HIS THR ILE PHE TRP PRO ASN MET ALA PRO PRO GLY LYS SEQRES 8 D 214 GLY GLY GLY THR PRO GLY GLY ARG VAL ALA ASP LEU ILE SEQRES 9 D 214 GLU LYS GLN PHE GLY GLY PHE GLU LYS PHE LYS ALA LEU SEQRES 10 D 214 PHE SER ALA ALA ALA LYS THR VAL GLU GLY VAL GLY TRP SEQRES 11 D 214 GLY VAL LEU ALA PHE ASP PRO LEU THR GLU GLU LEU ARG SEQRES 12 D 214 ILE LEU GLN VAL GLU LYS HIS ASN VAL LEU MET THR ALA SEQRES 13 D 214 GLY LEU VAL PRO ILE LEU VAL ILE ASP VAL TRP GLU HIS SEQRES 14 D 214 ALA TYR TYR LEU GLN TYR LYS ASN ASP ARG GLY SER TYR SEQRES 15 D 214 VAL GLU ASN TRP TRP ASN VAL VAL ASN TRP ASP ASP VAL SEQRES 16 D 214 GLU LYS ARG LEU GLU GLN ALA LEU ASN ASN ALA LYS PRO SEQRES 17 D 214 LEU TYR LEU LEU PRO GLN HET MN A 215 1 HET EDO A 216 4 HET EDO A 217 4 HET EDO A 218 4 HET EDO A 219 4 HET EDO A 220 4 HET MN B 215 1 HET EDO B 216 4 HET EDO B 217 4 HET EDO B 218 4 HET EDO B 219 4 HET MN C 215 1 HET EDO C 216 4 HET EDO C 217 4 HET EDO C 218 4 HET EDO C 219 4 HET MN D 215 1 HET EDO D 216 4 HET EDO D 217 4 HET EDO D 218 4 HET EDO D 219 4 HET EDO D 220 4 HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 4(MN 2+) FORMUL 6 EDO 18(C2 H6 O2) FORMUL 27 HOH *734(H2 O) HELIX 1 1 ILE A 24 LYS A 34 1 11 HELIX 2 2 LYS A 34 LYS A 55 1 22 HELIX 3 3 ASP A 61 TRP A 83 1 23 HELIX 4 4 GLY A 97 GLY A 109 1 13 HELIX 5 5 GLY A 110 THR A 124 1 15 HELIX 6 6 TRP A 167 ALA A 170 5 4 HELIX 7 7 TYR A 171 LYS A 176 1 6 HELIX 8 8 ASP A 178 TRP A 187 1 10 HELIX 9 9 ASN A 188 VAL A 190 5 3 HELIX 10 10 ASN A 191 ALA A 206 1 16 HELIX 11 11 LYS A 207 TYR A 210 5 4 HELIX 12 12 ILE B 24 LYS B 34 1 11 HELIX 13 13 LYS B 34 LYS B 55 1 22 HELIX 14 14 ASP B 61 TRP B 83 1 23 HELIX 15 15 GLY B 97 GLY B 109 1 13 HELIX 16 16 GLY B 110 THR B 124 1 15 HELIX 17 17 TRP B 167 ALA B 170 5 4 HELIX 18 18 TYR B 171 LYS B 176 1 6 HELIX 19 19 ASP B 178 TRP B 187 1 10 HELIX 20 20 ASN B 188 VAL B 190 5 3 HELIX 21 21 ASN B 191 ALA B 206 1 16 HELIX 22 22 LYS B 207 TYR B 210 5 4 HELIX 23 23 ILE C 24 LYS C 34 1 11 HELIX 24 24 LYS C 34 LYS C 55 1 22 HELIX 25 25 ASP C 61 TRP C 83 1 23 HELIX 26 26 GLY C 97 GLY C 109 1 13 HELIX 27 27 GLY C 110 THR C 124 1 15 HELIX 28 28 TRP C 167 ALA C 170 5 4 HELIX 29 29 TYR C 171 LYS C 176 1 6 HELIX 30 30 ASP C 178 TRP C 187 1 10 HELIX 31 31 ASN C 188 VAL C 190 5 3 HELIX 32 32 ASN C 191 TYR C 210 1 20 HELIX 33 33 ILE D 24 LYS D 34 1 11 HELIX 34 34 LYS D 34 LYS D 55 1 22 HELIX 35 35 ASP D 61 TRP D 83 1 23 HELIX 36 36 GLY D 97 GLY D 109 1 13 HELIX 37 37 GLY D 110 THR D 124 1 15 HELIX 38 38 TRP D 167 ALA D 170 5 4 HELIX 39 39 TYR D 171 LYS D 176 1 6 HELIX 40 40 ASP D 178 TRP D 187 1 10 HELIX 41 41 ASN D 188 VAL D 190 5 3 HELIX 42 42 ASN D 191 ALA D 206 1 16 HELIX 43 43 LYS D 207 TYR D 210 5 4 SHEET 1 A 3 GLU A 141 GLU A 148 0 SHEET 2 A 3 GLY A 129 ASP A 136 -1 N ASP A 136 O GLU A 141 SHEET 3 A 3 VAL A 159 ASP A 165 -1 O ILE A 161 N LEU A 133 SHEET 1 B 3 LEU B 142 GLU B 148 0 SHEET 2 B 3 GLY B 129 PHE B 135 -1 N ALA B 134 O ARG B 143 SHEET 3 B 3 VAL B 159 ASP B 165 -1 O LEU B 162 N LEU B 133 SHEET 1 C 3 LEU C 142 GLU C 148 0 SHEET 2 C 3 GLY C 129 PHE C 135 -1 N ALA C 134 O ARG C 143 SHEET 3 C 3 VAL C 159 ASP C 165 -1 O LEU C 162 N LEU C 133 SHEET 1 D 3 LEU D 142 GLU D 148 0 SHEET 2 D 3 GLY D 129 PHE D 135 -1 N ALA D 134 O ARG D 143 SHEET 3 D 3 VAL D 159 ASP D 165 -1 O LEU D 162 N LEU D 133 LINK NE2 HIS A 31 MN MN A 215 1555 1555 2.19 LINK NE2 HIS A 79 MN MN A 215 1555 1555 2.21 LINK OD2 ASP A 165 MN MN A 215 1555 1555 2.03 LINK NE2 HIS A 169 MN MN A 215 1555 1555 2.21 LINK MN MN A 215 O HOH A 223 1555 1555 2.12 LINK NE2 HIS B 31 MN MN B 215 1555 1555 2.18 LINK NE2 HIS B 79 MN MN B 215 1555 1555 2.19 LINK OD2 ASP B 165 MN MN B 215 1555 1555 2.04 LINK NE2 HIS B 169 MN MN B 215 1555 1555 2.27 LINK MN MN B 215 O HOH B 221 1555 1555 2.05 LINK NE2 HIS C 31 MN MN C 215 1555 1555 2.16 LINK NE2 HIS C 79 MN MN C 215 1555 1555 2.20 LINK OD2 ASP C 165 MN MN C 215 1555 1555 2.03 LINK NE2 HIS C 169 MN MN C 215 1555 1555 2.28 LINK MN MN C 215 O HOH C 220 1555 1555 1.99 LINK NE2 HIS D 31 MN MN D 215 1555 1555 2.19 LINK NE2 HIS D 79 MN MN D 215 1555 1555 2.19 LINK OD2 ASP D 165 MN MN D 215 1555 1555 2.08 LINK NE2 HIS D 169 MN MN D 215 1555 1555 2.22 LINK MN MN D 215 O HOH D 221 1555 1555 2.09 CISPEP 1 GLU A 20 PRO A 21 0 3.80 CISPEP 2 GLU B 20 PRO B 21 0 4.00 CISPEP 3 GLU C 20 PRO C 21 0 3.45 CISPEP 4 GLU D 20 PRO D 21 0 4.24 SITE 1 AC1 5 HIS A 31 HIS A 79 ASP A 165 HIS A 169 SITE 2 AC1 5 HOH A 223 SITE 1 AC2 6 GLU A 148 LYS A 149 HOH A 280 HOH A 284 SITE 2 AC2 6 GLU C 148 LYS C 149 SITE 1 AC3 6 PRO A 11 LEU A 12 TYR A 14 TYR A 16 SITE 2 AC3 6 EDO A 220 HOH A 465 SITE 1 AC4 5 HOH A 331 HOH A 371 EDO B 218 EDO C 218 SITE 2 AC4 5 EDO D 220 SITE 1 AC5 5 LYS A 34 HIS A 35 THR A 38 HOH A 488 SITE 2 AC5 5 ASN C 177 SITE 1 AC6 5 LEU A 9 PRO A 10 PRO A 11 HIS A 32 SITE 2 AC6 5 EDO A 217 SITE 1 AC7 5 HIS B 31 HIS B 79 ASP B 165 HIS B 169 SITE 2 AC7 5 HOH B 221 SITE 1 AC8 4 PRO B 21 ASN B 185 HOH B 271 HOH B 533 SITE 1 AC9 5 PRO B 11 LEU B 12 TYR B 14 TYR B 16 SITE 2 AC9 5 HOH B 703 SITE 1 BC1 5 EDO A 218 GLU B 148 LYS B 149 EDO C 218 SITE 2 BC1 5 GLU D 148 SITE 1 BC2 6 HIS B 35 TYR B 39 TRP B 167 GLU D 168 SITE 2 BC2 6 ARG D 179 EDO D 218 SITE 1 BC3 5 HIS C 31 HIS C 79 ASP C 165 HIS C 169 SITE 2 BC3 5 HOH C 220 SITE 1 BC4 7 PRO C 11 LEU C 12 TYR C 16 HIS C 32 SITE 2 BC4 7 HOH C 436 HOH C 570 HOH C 634 SITE 1 BC5 5 GLN C 107 PHE C 108 LEU C 142 ARG C 143 SITE 2 BC5 5 HOH C 251 SITE 1 BC6 10 EDO A 218 HOH A 331 ARG B 67 EDO B 218 SITE 2 BC6 10 ARG C 67 HOH C 255 HOH C 262 HOH C 388 SITE 3 BC6 10 HOH C 672 GLU D 148 SITE 1 BC7 6 TRP A 167 HOH A 488 GLY C 127 GLU C 168 SITE 2 BC7 6 ARG C 179 HOH C 555 SITE 1 BC8 5 HIS D 31 HIS D 79 ASP D 165 HIS D 169 SITE 2 BC8 5 HOH D 221 SITE 1 BC9 5 PRO D 96 GLY D 97 GLY D 98 TRP D 192 SITE 2 BC9 5 GLU D 196 SITE 1 CC1 5 THR C 124 ASP D 61 VAL D 62 ARG D 63 SITE 2 CC1 5 HOH D 258 SITE 1 CC2 5 PHE B 71 EDO B 219 HOH B 316 VAL D 125 SITE 2 CC2 5 GLY D 127 SITE 1 CC3 4 PRO D 11 LEU D 12 TYR D 14 TYR D 16 SITE 1 CC4 9 ARG A 67 EDO A 218 HOH A 371 GLU C 148 SITE 2 CC4 9 ARG D 67 HOH D 237 HOH D 269 HOH D 271 SITE 3 CC4 9 HOH D 403 CRYST1 69.064 71.782 76.853 90.00 91.81 90.00 P 1 21 1 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 0.014479 0.000000 0.000457 0.00000 SCALE2 0.000000 0.013931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013018 0.00000