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- PDB-6ans: Crystal structure of a putative uncharacterized protein from Burk... -

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Basic information

Entry
Database: PDB / ID: 6ans
TitleCrystal structure of a putative uncharacterized protein from Burkholderia cenocepacia
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / structural genomics / Burkholderia cenocepacia / phosphate / Seattle Structural Genomics Center for Infectious Disease
Function / homologyDomain of unknown function DUF1214 / Protein of unknown function (DUF1214) / PHOSPHATE ION / DUF1214 domain-containing protein
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a putative uncharacterized protein from Burkholderia cenocepacia
Authors: Bowatte, K. / Delker, S.L. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_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

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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
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,14122
Polymers175,0064
Non-polymers1,13418
Water13,890771
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07011
Polymers87,5032
Non-polymers5679
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-81 kcal/mol
Surface area27210 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07011
Polymers87,5032
Non-polymers5679
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-79 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 134.470, 98.080
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 27 or resid 29...
21(chain B and ((resid 6 through 7 and (name N...
31(chain C and (resid 6 through 27 or resid 29...
41(chain D and (resid 6 through 27 or resid 29...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLY(chain A and (resid 6 through 27 or resid 29...AA6 - 2727 - 48
12GLNGLNLEULEU(chain A and (resid 6 through 27 or resid 29...AA29 - 5250 - 73
13ARGARGPHEPHE(chain A and (resid 6 through 27 or resid 29...AA54 - 7275 - 93
14PROPROHISHIS(chain A and (resid 6 through 27 or resid 29...AA74 - 7695 - 97
15THRTHRTYRTYR(chain A and (resid 6 through 27 or resid 29...AA78 - 10199 - 122
16ARGARGARGARG(chain A and (resid 6 through 27 or resid 29...AA102123
17THRTHRPO4PO4(chain A and (resid 6 through 27 or resid 29...AA - E2 - 40123
18THRTHRPO4PO4(chain A and (resid 6 through 27 or resid 29...AA - E2 - 40123
19THRTHRPO4PO4(chain A and (resid 6 through 27 or resid 29...AA - E2 - 40123
110THRTHRPO4PO4(chain A and (resid 6 through 27 or resid 29...AA - E2 - 40123
21ARGARGALAALA(chain B and ((resid 6 through 7 and (name N...BB6 - 727 - 28
22MSEMSEPO4PO4(chain B and ((resid 6 through 7 and (name N...BB - I1 - 40122
23MSEMSEPO4PO4(chain B and ((resid 6 through 7 and (name N...BB - I1 - 40122
24MSEMSEPO4PO4(chain B and ((resid 6 through 7 and (name N...BB - I1 - 40122
25MSEMSEPO4PO4(chain B and ((resid 6 through 7 and (name N...BB - I1 - 40122
31ARGARGGLYGLY(chain C and (resid 6 through 27 or resid 29...CC6 - 2727 - 48
32GLNGLNLEULEU(chain C and (resid 6 through 27 or resid 29...CC29 - 5250 - 73
33ARGARGPHEPHE(chain C and (resid 6 through 27 or resid 29...CC54 - 7275 - 93
34PROPROHISHIS(chain C and (resid 6 through 27 or resid 29...CC74 - 7695 - 97
35THRTHRGLUGLU(chain C and (resid 6 through 27 or resid 29...CC78 - 14099 - 161
36ILEILEALAALA(chain C and (resid 6 through 27 or resid 29...CC141 - 142162 - 163
37ARGARGNANA(chain C and (resid 6 through 27 or resid 29...CC - M6 - 40127
38ARGARGNANA(chain C and (resid 6 through 27 or resid 29...CC - M6 - 40127
39ARGARGNANA(chain C and (resid 6 through 27 or resid 29...CC - M6 - 40127
310ARGARGNANA(chain C and (resid 6 through 27 or resid 29...CC - M6 - 40127
41ARGARGGLYGLY(chain D and (resid 6 through 27 or resid 29...DD6 - 2727 - 48
42GLNGLNLEULEU(chain D and (resid 6 through 27 or resid 29...DD29 - 5250 - 73
43ARGARGPHEPHE(chain D and (resid 6 through 27 or resid 29...DD54 - 7275 - 93
44PROPROHISHIS(chain D and (resid 6 through 27 or resid 29...DD74 - 7695 - 97
45THRTHRTYRTYR(chain D and (resid 6 through 27 or resid 29...DD78 - 10199 - 122
46ARGARGARGARG(chain D and (resid 6 through 27 or resid 29...DD102123
47ARGARGNANA(chain D and (resid 6 through 27 or resid 29...DD - R6 - 40127
48ARGARGNANA(chain D and (resid 6 through 27 or resid 29...DD - R6 - 40127
49ARGARGNANA(chain D and (resid 6 through 27 or resid 29...DD - R6 - 40127
410ARGARGNANA(chain D and (resid 6 through 27 or resid 29...DD - R6 - 40127

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Uncharacterized protein / BuceA.18021.a.A1


Mass: 43751.543 Da / Num. of mol.: 4 / Fragment: BuceA.18021.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL2258 / Plasmid: BuceA.18021.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4EDY7

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Non-polymers , 5 types, 789 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytic MCSG 1 screen, B1 (100 mM MES/sodium hydroxide, pH 6.5, 20% w/v PEG4000, 0.6 M sodium chloride), 20 mg/mL BuceA.18021.a.A1.PD00490 (SE-MET), cryoprotectant: 20% ethylene glycol, ...Details: Microlytic MCSG 1 screen, B1 (100 mM MES/sodium hydroxide, pH 6.5, 20% w/v PEG4000, 0.6 M sodium chloride), 20 mg/mL BuceA.18021.a.A1.PD00490 (SE-MET), cryoprotectant: 20% ethylene glycol, tray 290946 B1, puck QUF9-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 23, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→46.071 Å / Num. obs: 81463 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.863 % / Biso Wilson estimate: 29.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.099 / Χ2: 1.262 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.263.8820.5282.84118970.8790.61299.9
2.26-2.323.8870.4673.37116880.8930.54199.8
2.32-2.393.8930.3754.09112900.9270.43499.9
2.39-2.463.890.3144.85109060.950.364100
2.46-2.543.8930.2735.69106130.9590.316100
2.54-2.633.8980.2386.57102770.9680.276100
2.63-2.733.8980.1878.1399920.980.217100
2.73-2.843.9020.1569.5695300.9850.181100
2.84-2.973.8990.13610.992240.9880.157100
2.97-3.113.8950.11412.8787260.990.132100
3.11-3.283.8860.08715.8283280.9940.102100
3.28-3.483.8680.06918.9978220.9960.081100
3.48-3.723.8570.05821.7374150.9970.06799.9
3.72-4.023.8460.0524.3268440.9970.05899.9
4.02-4.43.8140.04126.7363500.9980.048100
4.4-4.923.7740.03728.2157030.9980.04399.7
4.92-5.683.7580.03827.3150460.9980.04499.6
5.68-6.963.6810.03926.4741640.9980.04697.9
6.96-9.843.680.03130.3132300.9980.03697.8
9.84-503.5960.02732.0617370.9980.03297.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PARROTphasing
ARPmodel building
Cootmodel building
PHENIXdev_2849refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.071 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 19
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 1970 2.42 %0, random
Rwork0.1504 ---
obs0.1513 81463 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.69 Å2 / Biso mean: 36.554 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 2.2→46.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11208 0 66 784 12058
Biso mean--32.53 39.69 -
Num. residues----1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811616
X-RAY DIFFRACTIONf_angle_d0.91115874
X-RAY DIFFRACTIONf_chiral_restr0.0581730
X-RAY DIFFRACTIONf_plane_restr0.0062096
X-RAY DIFFRACTIONf_dihedral_angle_d11.9126862
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6360X-RAY DIFFRACTION7.745TORSIONAL
12B6360X-RAY DIFFRACTION7.745TORSIONAL
13C6360X-RAY DIFFRACTION7.745TORSIONAL
14D6360X-RAY DIFFRACTION7.745TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.25510.19931150.168556805795
2.2551-2.31610.17651160.160257035819
2.3161-2.38420.21631340.156256785812
2.3842-2.46120.21351480.161756075755
2.4612-2.54910.21531680.164656215789
2.5491-2.65120.26711470.165556745821
2.6512-2.77180.22471220.1656705792
2.7718-2.9180.17271380.172256905828
2.918-3.10070.2421230.178357005823
3.1007-3.34010.19811620.166356215783
3.3401-3.67610.18211710.150156965867
3.6761-4.20770.16591710.129556395810
4.2077-5.30.14661170.116457515868
5.3-46.08080.17781380.150457635901
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)
12.2826-1.5021-0.81784.1894-0.36911.08660.07910.2625-0.3523-0.1237-0.1555-0.06330.14230.03070.07880.24650.0119-0.00740.3748-0.01350.270671.734665.333812.5043
21.4086-0.1095-0.00831.835-0.02221.0860.02490.19730.2554-0.0274-0.0733-0.1338-0.28430.14390.03760.2224-0.0318-0.02780.26940.0670.261560.28985.596720.4242
30.91850.09410.19840.7358-0.0410.7585-0.0060.12020.09990.0176-0.05180.1215-0.065-0.12330.04770.22750.01220.03720.3119-0.01930.263135.678460.5602-24.22
42.5571-1.17351.02743.5811-0.06611.18720.31130.55740.0663-0.6062-0.34160.2352-0.0639-0.09230.04250.30270.0818-0.03190.4588-0.01460.285922.550862.8728-40.481
51.4226-0.1774-0.01911.81920.16761.1350.00910.1806-0.2905-0.0086-0.09130.17240.2718-0.15380.06890.2188-0.0360.03620.2756-0.07280.283932.888944.3359-28.6463
60.72290.44760.55341.1498-0.21261.50760.003-0.08810.03680.0912-0.02670.0610.0156-0.1680.03220.1989-0.00180.02950.2790.00340.226740.91664.169428.233
72.6294-0.6810.01572.5348-0.14531.6828-0.00220.07350.2041-0.11250.07540.0549-0.1208-0.3738-0.08390.2191-0.01050.01520.35290.00430.283926.176170.873811.8401
81.10081.12351.95262.09911.52153.539-0.08770.08780.1516-0.36230.0367-0.0983-0.2814-0.00080.02990.2297-0.02730.07740.30530.05810.265137.252773.993510.0859
90.82050.02980.28892.37750.49171.61220.0263-0.0503-0.1712-0.0464-0.01050.09240.396-0.23250.00930.2862-0.05890.02280.28480.03190.234933.968950.931120.2099
101.41530.20691.02972.2240.96493.12080.09290.2577-0.2954-0.56270.0865-0.37760.580.135-0.14260.5563-0.04160.06070.2246-0.060.373540.205540.27746.8374
110.1844-0.2152-0.40220.9741.29731.9289-0.09410.1312-0.58010.0646-0.0430.24350.5927-0.13720.0990.5068-0.1155-0.00910.2587-0.02160.421533.421738.477811.5794
120.4491.5621-0.52538.314-1.36333.49530.0225-0.1233-0.10760.6079-0.1337-0.75590.21360.35240.12030.25370.0071-0.05690.3270.00160.279452.549659.6141-8.571
131.6846-0.2106-0.81451.53790.55591.77-0.0141-0.0433-0.0644-0.0181-0.03460.0944-0.12660.15550.04670.1905-0.0261-0.01760.24260.00350.202152.256668.3046-26.1858
142.7472-0.71650.18632.75110.09521.4654-0.01720.0492-0.2001-0.13650.0686-0.09520.14980.373-0.06130.21810.0052-0.0010.3471-0.00770.281167.10859.1009-37.0554
151.26690.8888-1.69891.574-0.59282.5371-0.10990.1107-0.1842-0.18930.09120.11890.0779-0.1243-0.03950.2165-0.0144-0.07140.3353-0.06790.272755.911556.2382-38.9297
160.84710.1056-0.26152.2855-0.56171.54440.03-0.02060.2179-0.0954-0.0005-0.0166-0.43540.1711-0.010.308-0.0509-0.01290.2361-0.02550.231257.882881.5605-32.0645
170.1906-0.18220.41780.9781-1.28421.9647-0.08110.07170.4902-0.0107-0.0033-0.2083-0.67850.12440.11040.5088-0.10540.02410.27460.00630.396259.93291.4552-37.3753
181.05770.1652-0.24770.83260.16190.6443-0.01140.1061-0.12480.0433-0.0557-0.1460.04340.10260.0760.22370.0114-0.0310.2970.01740.256457.421269.416924.8689
192.4705-1.14491.01335.1107-0.73187.35130.49560.78190.1914-1.1842-0.4698-0.0978-0.14220.2986-0.09570.36990.18240.0760.70150.05660.370869.383169.11263.6344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 152 through 175 )C152 - 175
2X-RAY DIFFRACTION2chain 'C' and (resid 176 through 365 )C176 - 365
3X-RAY DIFFRACTION3chain 'D' and (resid 6 through 129 )D6 - 129
4X-RAY DIFFRACTION4chain 'D' and (resid 130 through 175 )D130 - 175
5X-RAY DIFFRACTION5chain 'D' and (resid 176 through 365 )D176 - 365
6X-RAY DIFFRACTION6chain 'A' and (resid 2 through 94 )A2 - 94
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 175 )A95 - 175
8X-RAY DIFFRACTION8chain 'A' and (resid 176 through 202 )A176 - 202
9X-RAY DIFFRACTION9chain 'A' and (resid 203 through 302 )A203 - 302
10X-RAY DIFFRACTION10chain 'A' and (resid 303 through 338 )A303 - 338
11X-RAY DIFFRACTION11chain 'A' and (resid 339 through 369 )A339 - 369
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 31 )B1 - 31
13X-RAY DIFFRACTION13chain 'B' and (resid 32 through 94 )B32 - 94
14X-RAY DIFFRACTION14chain 'B' and (resid 95 through 175 )B95 - 175
15X-RAY DIFFRACTION15chain 'B' and (resid 176 through 202 )B176 - 202
16X-RAY DIFFRACTION16chain 'B' and (resid 203 through 338 )B203 - 338
17X-RAY DIFFRACTION17chain 'B' and (resid 339 through 369 )B339 - 369
18X-RAY DIFFRACTION18chain 'C' and (resid 6 through 129 )C6 - 129
19X-RAY DIFFRACTION19chain 'C' and (resid 130 through 151 )C130 - 151

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