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- PDB-3js4: Crystal structure of iron superoxide dismutase from Anaplasma pha... -

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Basic information

Entry
Database: PDB / ID: 3js4
TitleCrystal structure of iron superoxide dismutase from Anaplasma phagocytophilum
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / gram-negative bacteria / human granulocytic anaplasmosis / Fe / metalloenzyme
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Iron superoxide dismutase from Anaplasma phagocytophilum
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23312
Polymers101,9184
Non-polymers3158
Water11,584643
1
A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5583
Polymers25,4791
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5583
Polymers25,4791
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5583
Polymers25,4791
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5583
Polymers25,4791
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.660, 66.600, 85.440
Angle α, β, γ (deg.)102.090, 104.830, 88.580
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 206 / Label seq-ID: 22 - 227

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Superoxide dismutase


Mass: 25479.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: sodB, APH_0371 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2GKX4, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PACT screen condition E1, 20% PEG 3350, 0.2 M NaF. 0.4/0.4 microliter drops. 30.0 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% Glycerol, 2 mM DTT. Crystal tracking ID 204869e1, ...Details: PACT screen condition E1, 20% PEG 3350, 0.2 M NaF. 0.4/0.4 microliter drops. 30.0 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% Glycerol, 2 mM DTT. Crystal tracking ID 204869e1, expression tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 116074 / Num. obs: 63217 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.647 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 14.37
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 4640 / Num. unique all: 4284 / Num. unique obs: 4284 / % possible all: 83.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.32 Å42.95 Å
Translation2.32 Å42.95 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UNF

1unf


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.147 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 6.998 / SU ML: 0.092 / SU R Cruickshank DPI: 0.164 / SU Rfree: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3182 5 %RANDOM
Rwork0.167 ---
obs0.169 63217 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.22 Å2 / Biso mean: 12.299 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0.02 Å2-0.13 Å2
2--1.02 Å20.45 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 8 643 7160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216725
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9329167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4475830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29524.762336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.071151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7041518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215294
X-RAY DIFFRACTIONr_mcbond_it0.5521.54093
X-RAY DIFFRACTIONr_mcangle_it1.01726521
X-RAY DIFFRACTIONr_scbond_it1.78432632
X-RAY DIFFRACTIONr_scangle_it2.8534.52643
Refine LS restraints NCS

Ens-ID: 1 / Number: 1581 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.250.5
2BMEDIUM POSITIONAL0.280.5
3CMEDIUM POSITIONAL0.250.5
4DMEDIUM POSITIONAL0.270.5
1AMEDIUM THERMAL0.672
2BMEDIUM THERMAL0.672
3CMEDIUM THERMAL0.722
4DMEDIUM THERMAL0.782
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 233 -
Rwork0.227 4048 -
all-4281 -
obs--83.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.72410.77180.31560.7024-0.07841.147-0.0544-0.27830.20340.1030.02070.0318-0.0718-0.0810.03370.06930.01630.01030.0591-0.03690.02994.01281.756911.6805
22.66320.30720.54850.176-0.15890.76310.0150.01990.20120.0302-0.02230.0383-0.1155-0.00190.00730.0640.00940.01480.03540.00810.05984.07243.8110.4034
34.0522-2.10481.35922.8473-0.65822.3978-0.10410.3790.0349-0.08540.03240.15710.0585-0.20310.07180.0783-0.0265-0.02930.1780.02270.027-10.2841-3.1348-12.5642
41.5574-0.31450.34290.6729-0.02690.82180.02050.18070.0982-0.08460.013-0.0025-0.0336-0.0831-0.03350.05940.0060.01070.09050.03240.025-3.0824-1.8246-4.2713
53.8794-1.29060.0540.87160.06880.97140.04630.3620.2508-0.0924-0.0571-0.0053-0.03920.07580.01080.0732-0.01080.00750.06170.05220.0591-4.6946-14.5093-51.7544
63.6398-0.21570.53940.05840.12620.6532-0.0172-0.03340.3648-0.0355-0.003-0.0383-0.1169-0.0070.02030.0673-0.010.0080.0169-0.00230.1141-4.3622-12.6141-40.4649
74.70531.33711.85031.59091.15272.7227-0.0594-0.40430.11920.04420.0943-0.03350.14410.0647-0.0350.04210.0242-0.00680.1193-0.04220.01539.4754-20.0664-27.3903
81.92970.0782-0.18130.84530.29980.75130.0179-0.14490.2110.04870.00840.0009-0.02130.0547-0.02630.0587-0.00760.00360.0395-0.02210.05592.521-18.5131-35.966
91.69690.521.48121.28640.01013.51620.10540.0746-0.30740.06130.0141-0.22510.18090.3027-0.11950.03850.0124-0.00570.0307-0.00420.0907-0.9781-46.8269-42.2259
101.7405-0.01110.70540.7135-0.18221.08810.0362-0.1345-0.15720.0976-0.0171-0.01660.1034-0.0321-0.01910.0753-0.03130.00960.03020.01140.0616-11.8693-45.6511-38.8651
113.06672.8510.11155.61711.0141.4044-0.15430.17360.3597-0.42550.08820.501-0.1345-0.34170.06610.03840.0029-0.04950.13180.06820.1588-26.7417-38.3012-51.08
121.27190.4792-0.05320.9527-0.05360.6036-0.02090.03730.0347-0.04560.00850.1501-0.011-0.07460.01240.0448-0.01960.00070.04730.00430.063-17.5694-40.8815-45.7546
131.9296-0.6250.55810.8529-0.15932.26780.13340.1242-0.5139-0.1006-0.09960.25170.2569-0.2218-0.03380.0705-0.0245-0.03160.0504-0.05350.17340.4293-30.22680.7926
141.4957-0.65491.07380.5695-0.32862.40390.12410.2449-0.4205-0.0535-0.1380.12540.08840.07040.01390.09020.025-0.02040.1028-0.07550.207711.2991-28.8528-1.9563
155.4828-3.22430.98134.1447-1.57662.3523-0.0422-0.1061-0.110.20950.04270.1495-0.13290.2782-0.00060.0325-0.0275-0.00250.1006-0.0140.0625.9243-22.417211.5666
161.5561-0.50610.10230.90590.0690.58130.07070.0705-0.18710.0086-0.043-0.03010.03560.0565-0.02770.050.0052-0.00670.0563-0.00440.074916.5474-24.70845.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A50 - 98
3X-RAY DIFFRACTION3A99 - 124
4X-RAY DIFFRACTION4A125 - 206
5X-RAY DIFFRACTION5B1 - 49
6X-RAY DIFFRACTION6B50 - 98
7X-RAY DIFFRACTION7B99 - 124
8X-RAY DIFFRACTION8B125 - 206
9X-RAY DIFFRACTION9C1 - 49
10X-RAY DIFFRACTION10C50 - 98
11X-RAY DIFFRACTION11C99 - 124
12X-RAY DIFFRACTION12C125 - 206
13X-RAY DIFFRACTION13D1 - 49
14X-RAY DIFFRACTION14D50 - 98
15X-RAY DIFFRACTION15D99 - 124
16X-RAY DIFFRACTION16D125 - 206

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