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- PDB-4pup: 2.75 Angstrom resolution crystal structure of uncharacterized pro... -

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Basic information

Entry
Database: PDB / ID: 4pup
Title2.75 Angstrom resolution crystal structure of uncharacterized protein from Burkholderia cenocepacia J2315
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / Burkholderia cenocepacia J2315 / APC110287
Function / homologyNinX, bacteriophage P22 / Bacteriophage P22, NinX / DUF2591 domain-containing protein
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.75 Angstrom resolution crystal structure of uncharacterized protein from Burkholderia cenocepacia J2315
Authors: Halavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)42,7183
Polymers42,7183
Non-polymers00
Water1,00956
1
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,4792
Polymers28,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area10880 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,4792
Polymers28,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-6 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.785, 88.051, 79.375
Angle α, β, γ (deg.)90.00, 108.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEAA0 - 1207 - 127
21MSEMSEBB0 - 1207 - 127
12MSEMSEAA0 - 1207 - 127
22MSEMSECC0 - 1207 - 127
13PROPROBB0 - 1237 - 130
23PROPROCC0 - 1237 - 130

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Uncharacterized protein


Mass: 14239.280 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (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.: 56 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: protein: 7 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization conditions: 0.2 M Sodium formate, 20 % (w/v) PEG 3350, 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: Feb 27, 2014 / Details: Be lenses
RadiationMonochromator: Diamond / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 10997 / Num. obs: 10997 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 18.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.605 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→28.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.912 / SU B: 32.202 / SU ML: 0.298 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 4.067 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25497 523 4.8 %RANDOM
Rwork0.22436 ---
obs0.22589 10382 98.59 %-
all-10382 --
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: 56.312 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å20 Å20.81 Å2
2---0.4 Å20 Å2
3----4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.75→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 0 56 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192592
X-RAY DIFFRACTIONr_bond_other_d0.0060.022356
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9563538
X-RAY DIFFRACTIONr_angle_other_deg1.21135417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3185334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.01122.743113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28515321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6061523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212994
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02597
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53930.13
12B53930.13
21A53340.14
22C53340.14
31B57630.1
32C57630.1
LS refinement shellResolution: 2.751→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.557 28 -
Rwork0.343 752 -
obs--96.65 %
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)
13.54510.3790.52112.33440.91784.51850.1573-0.32-0.1204-0.0578-0.0692-0.2927-0.26470.9044-0.08810.033-0.0575-0.02740.3037-0.04130.155311.158140.70844.5734
25.6043-4.5978-6.295210.23587.81318.19-0.1467-0.7285-0.69410.1511-0.2371-0.1280.22810.53510.38390.22420.1183-0.07110.39910.07540.61817.61730.1654.9601
38.41833.5812.803223.066211.44336.95520.2326-0.2015-0.4063-0.47790.162-1.2681-0.0730.7633-0.39460.0640.0966-0.00810.48650.10250.252320.037636.38348.7574
44.3329-0.5008-2.31047.71651.40987.2190.0094-0.0184-0.2419-0.124-0.2484-0.05050.83180.3360.2390.3855-0.14940.01840.1970.00720.1892-12.417223.380526.9302
52.087-0.3465-0.5936.02230.50295.27710.18930.16040.1677-0.1977-0.14830.73530.0841-0.4881-0.04110.1678-0.1765-0.01180.2872-0.01870.4083-15.789338.209424.343
69.2285-1.696811.127110.0418-4.219714.56511.32420.1838-0.0615-0.7296-0.79950.07871.94450.2352-0.52470.6294-0.24520.03610.355-0.05150.404-19.618418.313729.9081
710.5264-1.5294-0.64353.77261.7692.60050.1736-0.64240.13850.30950.0479-0.0159-0.07080.7203-0.22150.3749-0.2492-0.01140.5389-0.11680.52178.223352.182524.5662
86.61750.58330.91441.1576-1.67473.35340.2678-0.06840.16210.24130.03370.1124-0.48530.1646-0.30150.2181-0.14840.04190.1655-0.06490.3372-4.935348.337822.3163
926.6197-6.749-5.60177.38591.28871.73570.0109-0.55550.22880.26050.25770.3717-0.19690.436-0.26860.2664-0.21950.00370.2762-0.0720.16438.475558.279522.1237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 74
2X-RAY DIFFRACTION2A75 - 104
3X-RAY DIFFRACTION3A105 - 121
4X-RAY DIFFRACTION4B-1 - 50
5X-RAY DIFFRACTION5B51 - 111
6X-RAY DIFFRACTION6B112 - 123
7X-RAY DIFFRACTION7C0 - 38
8X-RAY DIFFRACTION8C39 - 106
9X-RAY DIFFRACTION9C107 - 123

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