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- PDB-3bde: Crystal structure of a dabb family protein with a ferredoxin-like... -

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Basic information

Entry
Database: PDB / ID: 3bde
TitleCrystal structure of a dabb family protein with a ferredoxin-like fold (mll5499) from mesorhizobium loti maff303099 at 1.79 A resolution
ComponentsMll5499 protein
KeywordsUNKNOWN FUNCTION / Stress responsive a/b barrel domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Mll5499 protein
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of domain of unknown function with a ferredoxin-like fold (NP_106155.1) from Mesorhizobium loti at 1.79 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Jan 25, 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 1.5Nov 6, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mll5499 protein
B: Mll5499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,68418
Polymers28,6942
Non-polymers99016
Water4,558253
1
A: Mll5499 protein
hetero molecules

A: Mll5499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,80520
Polymers28,6942
Non-polymers1,11118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2110 Å2
MethodPISA
2
B: Mll5499 protein
hetero molecules

B: Mll5499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,56316
Polymers28,6942
Non-polymers86914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.669, 28.415, 76.985
Angle α, β, γ (deg.)90.000, 117.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-157-

HOH

21B-208-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Mll5499 protein


Mass: 14346.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_106155.1, mll5499 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98BN1
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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 MGSDKIHHHHHHENLYFQG.

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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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: NANODROP, 0.2M Na Acetate, 20.0% PEG 3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9797, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 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
10.95371
20.97971
30.97961
ReflectionResolution: 1.79→29.54 Å / Num. obs: 20638 / % possible obs: 94.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 18.85 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.79-1.841.60.4651.7184711530.46573.2
1.84-1.891.80.3432.2231412980.34383.3
1.89-1.9420.311.5268113260.3190
1.94-22.20.2323.3314014060.23295.3
2-2.072.40.1834.1331714080.18398.3
2.07-2.142.40.1554.9332013720.15598.5
2.14-2.222.50.1285.8327913270.12898.7
2.22-2.312.40.1176.2314412850.11799
2.31-2.412.50.1037.2304212310.10399.3
2.41-2.532.40.098.1287311790.0999.1
2.53-2.672.40.0819271211070.08199
2.67-2.832.40.0729.9263010780.07298.5
2.83-3.032.40.05911.623229650.05998.2
3.03-3.272.40.05112.322359290.05198.1
3.27-3.582.40.04613.220238570.04697.7
3.58-42.20.04414.416597520.04496.5
4-4.622.10.04313.413926700.04394.9
4.62-5.662.30.04213.913605860.04297.2
5.66-8.012.30.05112.310394450.05197.6
8.01-29.542.20.0538.85932640.05393.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→29.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.341 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.133
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. RESIDUES 98-101 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. ACT AND EDO MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1063 5.2 %RANDOM
Rwork0.177 ---
obs0.179 20637 94.02 %-
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: 16.841 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.51 Å2
2--0.38 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 64 253 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211774
X-RAY DIFFRACTIONr_bond_other_d0.0040.021257
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9382379
X-RAY DIFFRACTIONr_angle_other_deg1.26933020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2455208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50222.74791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.16615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5821513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02397
X-RAY DIFFRACTIONr_nbd_refined0.1780.2302
X-RAY DIFFRACTIONr_nbd_other0.1450.21185
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2830
X-RAY DIFFRACTIONr_nbtor_other0.0750.2888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.220
X-RAY DIFFRACTIONr_mcbond_it1.93531142
X-RAY DIFFRACTIONr_mcbond_other0.4473400
X-RAY DIFFRACTIONr_mcangle_it2.54751648
X-RAY DIFFRACTIONr_scbond_it4.368829
X-RAY DIFFRACTIONr_scangle_it5.63111725
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 50 -
Rwork0.241 1103 -
all-1153 -
obs--72.38 %
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)
11.1542-0.1290.30460.3371-0.08010.63490.01810.002-0.03340.0297-0.0094-0.01620.00560.015-0.0087-0.02340.00560.0044-0.03770.0097-0.024610.68678.27024.6276
20.6332-0.0390.61470.4326-0.08961.0319-0.0058-0.022-0.01630.03990.02350.02520.0054-0.0101-0.0177-0.01280.00410.0048-0.01780.0126-0.021131.82150.686327.782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9820 - 117
2X-RAY DIFFRACTION2BB1 - 9820 - 117

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