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- PDB-3dcz: CRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPOR... -

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Basic information

Entry
Database: PDB / ID: 3dcz
TitleCRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX (TM0246) FROM THERMOTOGA MARITIMA AT 1.65 A RESOLUTION
Componentsputative RnfG subunit of electron transport complex
KeywordsOXIDOREDUCTASE / PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Translocases / oxidoreductase complex / oxidoreductase activity, acting on NAD(P)H / electron transport chain / FMN binding / electron transfer activity / plasma membrane
Similarity search - Function
Ion-translocating oxidoreductase complex, subunit RnfG/RsxG / FMN-binding / FMN-binding domain / FMN_bind
Similarity search - Domain/homology
ACETATE ION / Ion-translocating oxidoreductase complex subunit G
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative RnfG subunit of electron transport complex (TM0246) from THERMOTOGA MARITIMA at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative RnfG subunit of electron transport complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2925
Polymers22,9791
Non-polymers3134
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.125, 103.827, 44.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein putative RnfG subunit of electron transport complex


Mass: 22978.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0246 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WY88
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 30-224 OF THE FULL LENGTH PROTEIN.

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25.0% polyethylene glycol 4000, 0.2M ammonium sulfate, 0.1M sodium acetate pH 4.6, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97932,0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.978911
ReflectionResolution: 1.65→29.148 Å / Num. obs: 25591 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.735 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.693.70.4971.5688518760.497100
1.69-1.743.70.4041.9666218080.404100
1.74-1.793.70.3192.4652417720.319100
1.79-1.843.70.2662.9633617170.266100
1.84-1.913.70.2173.5620616800.217100
1.91-1.973.70.1634.4590716120.163100
1.97-2.053.70.1335.6580415580.133100
2.05-2.133.70.116.7549914910.11100
2.13-2.223.70.0937.6539914640.093100
2.22-2.333.70.0937.5514613900.093100
2.33-2.463.70.0926.9482913190.092100
2.46-2.613.60.0867.5452012400.086100
2.61-2.793.60.0768.8430611840.076100
2.79-3.013.70.06210.2405411080.062100
3.01-3.33.70.05111.6376010270.051100
3.3-3.693.60.04314.233389220.043100
3.69-4.263.60.04114.529898280.041100
4.26-5.223.60.0371625207050.037100
5.22-7.383.50.04115.219945690.041100
7.38-29.153.30.04114.510453210.04197.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.148 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.023 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SO4,ACT,EDO MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1304 5.1 %RANDOM
Rwork0.176 ---
obs0.177 25581 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 18 145 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221404
X-RAY DIFFRACTIONr_bond_other_d0.0050.02959
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.011915
X-RAY DIFFRACTIONr_angle_other_deg0.89832364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76524.10756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.145159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined0.2160.2268
X-RAY DIFFRACTIONr_nbd_other0.1990.2969
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2673
X-RAY DIFFRACTIONr_nbtor_other0.0870.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.218
X-RAY DIFFRACTIONr_mcbond_it2.0533906
X-RAY DIFFRACTIONr_mcbond_other0.4893356
X-RAY DIFFRACTIONr_mcangle_it2.98951433
X-RAY DIFFRACTIONr_scbond_it4.2568553
X-RAY DIFFRACTIONr_scangle_it6.11411470
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 105 -
Rwork0.223 1771 -
all-1876 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 31.2107 Å / Origin y: 35.4521 Å / Origin z: 18.5391 Å
111213212223313233
T-0.0385 Å2-0.0145 Å2-0.0078 Å2--0.0296 Å2-0.0066 Å2---0.0461 Å2
L1.2594 °20.0061 °2-0.528 °2-1.3301 °20.2736 °2--1.0959 °2
S0.0064 Å °-0.0414 Å °0.0615 Å °0.0989 Å °-0.0045 Å °-0.0051 Å °0.0431 Å °-0.0387 Å °-0.0019 Å °

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