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- PDB-3bf4: Crystal structure of an ethd-like protein (reut_b5694) from ralst... -

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Basic information

Entry
Database: PDB / ID: 3bf4
TitleCrystal structure of an ethd-like protein (reut_b5694) from ralstonia eutropha jmp134 at 2.10 A resolution
ComponentsEthyl tert-butyl ether degradation EthD protein
KeywordsUNKNOWN FUNCTION / Ferredoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
EthD domain / EthD domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Ethyl tert-butyl ether degradation EthD
Similarity search - Component
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of EthD-like protein (YP_299883.1) from Ralstonia eutropha JMP134 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: 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 1.4Oct 20, 2021Group: 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 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: Q72Y, Q76Y, E77Y.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethyl tert-butyl ether degradation EthD protein
B: Ethyl tert-butyl ether degradation EthD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4638
Polymers29,0932
Non-polymers3706
Water3,297183
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 74.540, 98.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU4AA0 - 8119 - 100
21GLYGLYGLUGLU4BB0 - 8119 - 100
32ILEILEARGARG6AA82 - 108101 - 127
42ILEILEARGARG6BB82 - 108101 - 127

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Components

#1: Protein Ethyl tert-butyl ether degradation EthD protein


Mass: 14546.386 Da / Num. of mol.: 2 / Mutation: Q72Y, Q76Y, E77Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Species: Cupriavidus necator / Gene: YP_299883.1, Reut_B5694 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46P95
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT WAS ENGINEERED WITH REMARK 999 THE FOLLOWING MUTATIONS: Q72Y, Q76Y, E77Y.

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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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 15.0% Glycerol, 8.5% Isopropanol, 17.0% PEG 4000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9184, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007 / Details: KOHZU: Double crystal Si(111)
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.91841
30.97961
ReflectionResolution: 2.1→29.761 Å / Num. obs: 16887 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.6532.1105232793195.8
2.17-2.260.5392.51247832801100
2.26-2.360.4752.91150030111100
2.36-2.490.3593.81259332941100
2.49-2.640.255.2114292987199.9
2.64-2.850.1727.41228332151100
2.85-3.130.1111.1115233046199.8
3.13-3.590.06716.1117873160199.5
3.59-4.510.04322.4111773052198.4
4.51-29.7610.03824.4107042977193.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.761 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.568 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. EDO AND IPA MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED. 5. THERE ARE SOME UNMODELED DENSITIES NEAR RESIDUES B51-52.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 849 5 %RANDOM
Rwork0.178 ---
obs0.179 16836 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 24 183 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221823
X-RAY DIFFRACTIONr_bond_other_d0.0060.021202
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9542470
X-RAY DIFFRACTIONr_angle_other_deg1.31732904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0125232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7823.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3615264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7831510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022085
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
X-RAY DIFFRACTIONr_nbd_refined0.1690.2303
X-RAY DIFFRACTIONr_nbd_other0.1350.21128
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2875
X-RAY DIFFRACTIONr_nbtor_other0.0710.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1080.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.28
X-RAY DIFFRACTIONr_mcbond_it1.59231291
X-RAY DIFFRACTIONr_mcbond_other0.4193461
X-RAY DIFFRACTIONr_mcangle_it2.13451814
X-RAY DIFFRACTIONr_scbond_it3.768784
X-RAY DIFFRACTIONr_scangle_it4.94811653
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1027MEDIUM POSITIONAL0.330.5
324LOOSE POSITIONAL0.485
1027MEDIUM THERMAL0.772
324LOOSE THERMAL1.8510
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 60 -
Rwork0.23 1154 -
all-1214 -
obs--99.18 %
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)
11.84620.1625-0.10272.7472-1.3553.5906-0.16750.16690.136-0.36570.0263-0.07080.1352-0.04660.1412-0.15460.01580.0643-0.2389-0.0212-0.293618.6527.86517.425
21.35490.2325-0.01952.383-1.17382.1302-0.0892-0.0216-0.1679-0.09380.0352-0.10910.1451-0.01920.0541-0.22210.0230.0516-0.2952-0.014-0.326617.35118.29732.505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-6 - 10813 - 127
2X-RAY DIFFRACTION2BB-2 - 10817 - 127

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