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- PDB-2gf4: Crystal structure of Vng1086c from Halobacterium salinarium (Halo... -

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Basic information

Entry
Database: PDB / ID: 2gf4
TitleCrystal structure of Vng1086c from Halobacterium salinarium (Halobacterium halobium). Northeast Structural Genomics Target HsR14
ComponentsProtein Vng1086c
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hsr14 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0058 / Uncharacterised protein family UPF0058 / Uncharacterised UPF0058 superfamily / Uncharacterised protein family UPF0058 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsBenach, J. / Zhou, W. / Jayaraman, S. / Forouhar, F.F. / Janjua, H. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. ...Benach, J. / Zhou, W. / Jayaraman, S. / Forouhar, F.F. / Janjua, H. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Vng1086c from Halobacterium salinarium (Halobacterium halobium). Northeast Structural Genomics Target HsR14
Authors: Benach, J. / Zhou, W. / Jayaraman, S. / Forouhar, F.F. / Janjua, H. / Xiao, R. / Ma, L.-C. / Cunningham, K. / Wang, D. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Vng1086c
B: Protein Vng1086c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5096
Polymers23,3102
Non-polymers1984
Water2,702150
1
A: Protein Vng1086c
B: Protein Vng1086c
hetero molecules

A: Protein Vng1086c
B: Protein Vng1086c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,01712
Polymers46,6214
Non-polymers3968
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8670 Å2
ΔGint-93 kcal/mol
Surface area15790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.669, 64.914, 123.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: x, -y, -z

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Components

#1: Protein Protein Vng1086c


Mass: 11655.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium sp. (Halophile) / Species: Halobacterium salinarum / Strain: NRC-1 / Gene: VNG1086C / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: Q9HQM9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: under oil / pH: 5
Details: 0.55M Calcium acetate 0.1 M Sodium acetate; 1ul+1ul used 25% ethylene glycol as cryoprotectant (1.5ul mother liquor + 0.5ul 100% EG), pH 5.0, Under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97877 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Av σ(I) over netI: 9.2 / Number: 159459 / Rmerge(I) obs: 0.098 / Χ2: 1.03 / D res high: 2 Å / D res low: 20 Å / Num. obs: 29978 / % possible obs: 99.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
22.07299298.80.4511.0274.3
4.320298499.10.0730.9975.9
3.424.3299999.90.0730.9816
2.993.42302599.90.0851.0425.9
2.712.99297799.90.1141.0525.6
2.522.71300899.90.1361.0445.4
2.372.5229961000.1771.0525.3
2.252.3730211000.2221.0425.2
2.152.25297799.90.3041.0655
2.072.15299999.70.3921.0644.7
ReflectionResolution: 2→20 Å / Num. obs: 29978 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.07 Å / % possible obs: 98.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.451 / Num. unique obs: 2992 / Χ2: 1.027 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se19.1920.6830.4930.0131.027
2Se23.1960.6480.0130.0141.05
3Se20.8970.2550.0330.0750.882
4Se30.0860.0770.4670.0751.184
5Se23.8980.1990.0730.0940.696
6Se41.9440.1340.4260.0940.835
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.6 / Reflection: 13220 / Reflection acentric: 11878 / Reflection centric: 1342
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.9-19.9940.840.860.77650479171
3.7-5.90.830.850.7319431645298
3-3.70.770.780.6823822115267
2.6-30.650.660.5322922081211
2.2-2.60.480.480.4638283550278
2.1-2.20.260.260.2921252008117

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→20 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2213 8.1 %RANDOM
Rwork0.226 ---
obs0.226 22937 83.9 %-
all-22937 --
Solvent computationBsol: 54.36 Å2
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2---10.856 Å20 Å2
3---7.886 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 10 150 1455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 44

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.07-2.090.371430.286326369
2.09-2.10.225320.226314346
2.1-2.120.208500.25383433
2.12-2.140.326350.276360395
2.14-2.150.285350.282369404
2.15-2.170.275480.261374422
2.17-2.190.198480.253348396
2.19-2.210.297440.251393437
2.21-2.230.252370.288371408
2.23-2.260.245540.254430484
2.26-2.280.265420.247413455
2.28-2.30.211550.222427482
2.3-2.330.392260.231446472
2.33-2.350.202380.239424462
2.35-2.380.223430.207472515
2.38-2.410.3460.226462508
2.41-2.440.296490.241419468
2.44-2.470.178390.25443482
2.47-2.50.311410.277499540
2.5-2.530.291540.22480534
2.53-2.570.27440.232487531
2.57-2.610.343450.243462507
2.61-2.650.216550.262464519
2.65-2.690.237620.238522584
2.69-2.740.259660.254475541
2.74-2.790.223510.231485536
2.79-2.840.217800.217473553
2.84-2.90.231560.231540596
2.9-2.960.245400.251498538
2.96-3.030.237860.22498584
3.03-3.110.262630.213545608
3.11-3.190.304440.218526570
3.19-3.280.265430.192563606
3.28-3.390.248350.221571606
3.39-3.510.192600.219526586
3.51-3.650.233600.214566626
3.65-3.810.252550.2540595
3.81-4.010.236540.207560614
4.01-4.260.146530.183554607
4.26-4.590.234620.209546608
4.59-5.040.234480.206545593
5.04-5.760.217490.235549598
5.76-7.20.193750.247549624
7.2-200.243680.257527595
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PAR
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4ACT_XPLOR_PAR.TXT

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