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- PDB-4qyb: 2.1 Angstrom resolution crystal structure of uncharacterized prot... -

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Basic information

Entry
Database: PDB / ID: 4qyb
Title2.1 Angstrom resolution crystal structure of uncharacterized protein, disulfide-bridged dimer, from Burkholderia cenocepacia J2315
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyNinX, bacteriophage P22 / Bacteriophage P22, NinX / DUF2591 domain-containing protein
Function and homology information
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.1 Angstrom resolution crystal structure of uncharacterized protein, disulfide-bridged dimer, from Burkholderia cenocepacia J2315
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,9272
Non-polymers00
Water1,40578
1
A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)53,8544
Polymers53,8544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5230 Å2
ΔGint-10 kcal/mol
Surface area21830 Å2
MethodPISA
2
A: Uncharacterized protein

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area1720 Å2
ΔGint-5 kcal/mol
Surface area11810 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-1 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.945, 85.634, 93.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 118 / Label seq-ID: 7 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Uncharacterized protein


Mass: 13463.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: BCAM1129 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: B4EGA9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, ...Details: protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: Be lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 14651 / Num. obs: 14651 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 49.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.3 / Num. unique all: 746 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUP

4pup


Resolution: 2.1→28.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.235 / SU ML: 0.192 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25648 717 5 %RANDOM
Rwork0.21094 ---
obs0.21315 13578 92.1 %-
all-13578 --
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: 54.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20 Å2
2--5.23 Å20 Å2
3----6.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 78 1805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191788
X-RAY DIFFRACTIONr_bond_other_d0.0040.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.952439
X-RAY DIFFRACTIONr_angle_other_deg0.97733734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.565230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58622.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5931519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212079
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02426
Refine LS restraints NCS

Ens-ID: 1 / Number: 5727 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 47 -
Rwork0.228 969 -
obs-969 90.96 %
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)
126.8228-5.868-10.67851.6232-0.004520.67630.5640.08521.5843-0.0892-0.1663-0.3502-0.38251.1436-0.39780.1823-0.05480.04580.16950.0850.252.6659-26.737-20.2311
23.1671-1.1665-0.90753.4234-0.26694.86460.030.27640.2945-0.1615-0.0612-0.01-0.55820.05660.03120.2895-0.0226-0.00240.0480.04040.3472-8.4156-16.0657-16.4937
31.6617-0.10580.23042.1786-0.71393.2787-0.1084-0.05640.1838-0.17060.10050.0589-0.2978-0.14080.00790.14940.0157-0.01170.054-0.00630.3137-13.4689-25.3748-6.7193
42.641-0.1776-0.24861.0447-1.7554.7039-0.02640.1189-0.1065-0.2552-0.0202-0.1552-0.20620.01360.04660.3511-0.0070.03850.07280.00310.3808-8.493-29.7192-13.0003
56.0648-2.07950.67735.19321.25718.31540.15160.0357-0.1912-0.3167-0.0260.04420.8383-0.5133-0.12560.2746-0.1496-0.01980.10650.01690.3418-26.4915-63.7865-15.4739
61.27811.67070.73884.2713-1.07743.3591-0.08140.0552-0.1615-0.63020.208-0.20990.83720.0278-0.12660.4022-0.06190.00210.0798-0.04150.3593-18.178-67.5651-9.1995
70.93820.8019-3.20181.9938-2.402311.08460.0969-0.02580.0557-0.08340.00550.0947-0.3884-0.0096-0.10250.06610.0167-0.01630.1944-0.01950.2709-17.624-48.7826-4.7751
80.7882-0.34520.18522.88461.98974.88760.0256-0.07080.1215-0.4273-0.07630.13420.2483-0.34610.05070.1706-0.0299-0.05660.09380.00960.3122-23.1898-55.6265-11.2246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 3
2X-RAY DIFFRACTION2A4 - 37
3X-RAY DIFFRACTION3A38 - 80
4X-RAY DIFFRACTION4A86 - 118
5X-RAY DIFFRACTION5B0 - 25
6X-RAY DIFFRACTION6B26 - 66
7X-RAY DIFFRACTION7B67 - 87
8X-RAY DIFFRACTION8B88 - 118

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