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- PDB-2amu: CRYSTAL STRUCTURE OF A PUTATIVE SUPEROXIDE REDUCTASE (TM0658) FRO... -

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Basic information

Entry
Database: PDB / ID: 2amu
TitleCRYSTAL STRUCTURE OF A PUTATIVE SUPEROXIDE REDUCTASE (TM0658) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION
ComponentsPutative superoxide reductase
KeywordsOXIDOREDUCTASE / PUTATIVE SUPEROXIDE REDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / iron ion binding
Similarity search - Function
: / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Putative superoxide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative superoxide reductase (EC 1.15.1.2) (SOR) (tm0658) from THERMOTOGA MARITIMA at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative superoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4742
Polymers16,4191
Non-polymers561
Water1,13563
1
A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9494
Polymers32,8372
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2540 Å2
ΔGint-10 kcal/mol
Surface area12800 Å2
MethodPISA
2
A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8988
Polymers65,6744
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12310 Å2
ΔGint-59 kcal/mol
Surface area18380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.618, 77.305, 64.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21A-226-

HOH

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Components

#1: Protein Putative superoxide reductase / SOR


Mass: 16418.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0658 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZC6, superoxide reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.1 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 10.0% Glycerol, 5.0% PEG-1000, 30.0% PEG-600, 0.1M MES , pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 4, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 2→28.07 Å / Num. obs: 8148 / % possible obs: 88.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2-2.0554.71.80.4011.93560.401
2.05-2.1163.520.352.14140.35
2.11-2.1769.92.10.3172.14290.317
2.17-2.2478.42.40.2952.64790.295
2.24-2.3186.42.70.2562.85170.256
2.31-2.3994.63.10.2143.55590.214
2.39-2.481003.60.2343.35600.234
2.48-2.581003.70.193.95440.19
2.58-2.799.93.60.1764.35160.176
2.7-2.8399.93.70.126.25000.12
2.83-2.9899.73.70.1027.24760.102
2.98-3.1699.83.60.0769.54460.076
3.16-3.3899.53.70.0611.44150.06
3.38-3.6599.53.70.052123930.052
3.65-499.23.60.042153690.042
4-4.4798.83.60.04314.23240.043
4.47-5.1698.43.60.04214.73010.042
5.16-6.3298.23.50.03715.72480.037
6.32-8.9497.13.50.03714.61910.037
8.94-28.0791.53.10.03214.81110.032

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1do6

1do6


Resolution: 2→28.07 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.304 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 385 4.7 %RANDOM
Rwork0.147 ---
all0.149 ---
obs-7762 88.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.878 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---1.28 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 1 63 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221086
X-RAY DIFFRACTIONr_bond_other_d0.0010.02721
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9421480
X-RAY DIFFRACTIONr_angle_other_deg1.28431777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42325.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9515184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.742153
X-RAY DIFFRACTIONr_chiral_restr0.1980.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_nbd_refined0.1740.2148
X-RAY DIFFRACTIONr_nbd_other0.1920.2701
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2494
X-RAY DIFFRACTIONr_nbtor_other0.090.2573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.211
X-RAY DIFFRACTIONr_mcbond_it2.0383729
X-RAY DIFFRACTIONr_mcbond_other0.4763264
X-RAY DIFFRACTIONr_mcangle_it2.78851093
X-RAY DIFFRACTIONr_scbond_it4.9668468
X-RAY DIFFRACTIONr_scangle_it5.86611386
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 19 -
Rwork0.202 336 -
obs--53.38 %
Refinement TLS params.Method: refined / Origin x: 15.954 Å / Origin y: 36.48 Å / Origin z: 23.076 Å
111213212223313233
T-0.1561 Å2-0.0412 Å2-0.0141 Å2--0.1873 Å2-0.033 Å2---0.0865 Å2
L1.857 °2-0.4699 °20.304 °2-3.0106 °2-1.122 °2--1.9576 °2
S-0.1029 Å °0.225 Å °-0.084 Å °-0.2564 Å °0.0457 Å °0.2374 Å °0.0944 Å °-0.1614 Å °0.0571 Å °

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