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- PDB-2ga1: Crystal structure of a duf433 member protein (ava_0674) from anab... -

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Basic information

Entry
Database: PDB / ID: 2ga1
TitleCrystal structure of a duf433 member protein (ava_0674) from anabaena variabilis atcc 29413 at 2.00 A resolution
ComponentsProtein of unknown function DUF433
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Alr1493-like domains / Protein of unknown function DUF433 / Protein of unknown function (DUF433) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DUF433 domain-containing protein
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (YP_321193.1) from Anabaena variabilis ATCC 29413 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of unknown function DUF433
B: Protein of unknown function DUF433
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1633
Polymers24,0702
Non-polymers921
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-21 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.980, 65.120, 86.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein of unknown function DUF433


Mass: 12035.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: YP_321193.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 75700622, UniProt: Q3MFD8*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 20.0% Glycerol, 0.16M Mg(oAc)2, 16.0% PEG-8000, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.978489, 0.979094
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2006
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Si(111) 2-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9784891
30.9790941
ReflectionResolution: 2→28.64 Å / Num. obs: 18535 / % possible obs: 99.1 % / Redundancy: 3.549 % / Biso Wilson estimate: 32.644 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.070.3422.335734301297.3
2.07-2.150.2293.56088319594.3
2.15-2.250.1744.46496339895.2
2.25-2.370.1335.66508341096.7
2.37-2.520.1096.56533341397.1
2.52-2.710.0838.16370333097.5
2.71-2.990.05910.46673349598
2.99-3.420.04513.66534340398.7
3.420.03717.26541343099.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.879 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.144
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL WAS MODELED INTO THE STRUCTURE BASED ON THE CRYSTALLIZATION CONDITIONS. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 958 5.2 %RANDOM
Rwork0.176 ---
obs0.178 18491 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.739 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2---0.7 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 6 200 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221676
X-RAY DIFFRACTIONr_bond_other_d0.0010.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9622296
X-RAY DIFFRACTIONr_angle_other_deg0.85233575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49825.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9421511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02305
X-RAY DIFFRACTIONr_nbd_refined0.2180.2379
X-RAY DIFFRACTIONr_nbd_other0.1680.21525
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2830
X-RAY DIFFRACTIONr_nbtor_other0.0850.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.212
X-RAY DIFFRACTIONr_mcbond_it2.25631137
X-RAY DIFFRACTIONr_mcbond_other0.5333411
X-RAY DIFFRACTIONr_mcangle_it2.99551683
X-RAY DIFFRACTIONr_scbond_it5.0978705
X-RAY DIFFRACTIONr_scangle_it6.74811606
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 57 -
Rwork0.216 1268 -
obs-1325 97.64 %
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)
10.6027-0.3373-0.04822.7011-1.6522.1458-0.0904-0.03040.03450.00850.08220.06960.0052-0.10320.0081-0.15290.0036-0.0016-0.1417-0.0089-0.118142.540943.437218.4693
23.9203-0.9788-2.71990.47930.82111.97290.270.22070.1412-0.2309-0.17760.0106-0.3599-0.1472-0.0924-0.03010.0426-0.0389-0.06390.0036-0.096925.572635.736642.3001
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1021 - 103
22BB1 - 1012 - 102

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