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- PDB-5vm1: Crystal structure of a xyloylose kinase from Brucella ovis -

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Basic information

Entry
Database: PDB / ID: 5vm1
TitleCrystal structure of a xyloylose kinase from Brucella ovis
ComponentsXylulokinase
KeywordsTRANSFERASE / NIAID / structural genomics / brucellosis / kinase / ATP-dependent / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


xylulokinase / xylulose catabolic process / D-xylulokinase activity / D-xylose metabolic process / ATP binding
Similarity search - Function
Xylulokinase / : / FGGY family of carbohydrate kinases signature 1. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain ...Xylulokinase / : / FGGY family of carbohydrate kinases signature 1. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a xyloylose kinase from
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Letesson, J.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Xylulokinase
B: Xylulokinase
C: Xylulokinase
D: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)209,2924
Polymers209,2924
Non-polymers00
Water2,432135
1
A: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)52,3231
Polymers52,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)52,3231
Polymers52,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)52,3231
Polymers52,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)52,3231
Polymers52,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Xylulokinase

C: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)104,6462
Polymers104,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area32730 Å2
MethodPISA
6
B: Xylulokinase

D: Xylulokinase


Theoretical massNumber of molelcules
Total (without water)104,6462
Polymers104,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2300 Å2
ΔGint-16 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.660, 167.070, 117.830
Angle α, β, γ (deg.)90.000, 101.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 or (resid 1 and (name...
21(chain B and (resid 0 through 31 or (resid 32...
31(chain C and (resid 0 or (resid 1 and (name...
41(chain D and (resid 0 or (resid 1 and (name...

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
11HISHISHISHIS(chain A and (resid 0 or (resid 1 and (name...AA08
12METMETMETMET(chain A and (resid 0 or (resid 1 and (name...AA19
13HISHISASPASP(chain A and (resid 0 or (resid 1 and (name...AA0 - 4838 - 491
14HISHISASPASP(chain A and (resid 0 or (resid 1 and (name...AA0 - 4838 - 491
15HISHISASPASP(chain A and (resid 0 or (resid 1 and (name...AA0 - 4838 - 491
16HISHISASPASP(chain A and (resid 0 or (resid 1 and (name...AA0 - 4838 - 491
21HISHISLEULEU(chain B and (resid 0 through 31 or (resid 32...BB0 - 318 - 39
22ASPASPASPASP(chain B and (resid 0 through 31 or (resid 32...BB3240
23HISHISASPASP(chain B and (resid 0 through 31 or (resid 32...BB0 - 4838 - 491
24HISHISASPASP(chain B and (resid 0 through 31 or (resid 32...BB0 - 4838 - 491
25HISHISASPASP(chain B and (resid 0 through 31 or (resid 32...BB0 - 4838 - 491
26HISHISASPASP(chain B and (resid 0 through 31 or (resid 32...BB0 - 4838 - 491
31HISHISHISHIS(chain C and (resid 0 or (resid 1 and (name...CC08
32METMETMETMET(chain C and (resid 0 or (resid 1 and (name...CC19
33HISHISASPASP(chain C and (resid 0 or (resid 1 and (name...CC0 - 4838 - 491
34HISHISASPASP(chain C and (resid 0 or (resid 1 and (name...CC0 - 4838 - 491
35HISHISASPASP(chain C and (resid 0 or (resid 1 and (name...CC0 - 4838 - 491
36HISHISASPASP(chain C and (resid 0 or (resid 1 and (name...CC0 - 4838 - 491
41HISHISHISHIS(chain D and (resid 0 or (resid 1 and (name...DD08
42METMETMETMET(chain D and (resid 0 or (resid 1 and (name...DD19
43HISHISASPASP(chain D and (resid 0 or (resid 1 and (name...DD0 - 4838 - 491
44HISHISASPASP(chain D and (resid 0 or (resid 1 and (name...DD0 - 4838 - 491
45HISHISASPASP(chain D and (resid 0 or (resid 1 and (name...DD0 - 4838 - 491
46HISHISASPASP(chain D and (resid 0 or (resid 1 and (name...DD0 - 4838 - 491

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Components

#1: Protein
Xylulokinase


Mass: 52322.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: xylB, BOV_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3APL8, xylulokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BrovA.00232.a.B1.PS02131 at 15.8 mg/mL against MCSG1 screen condition B3 0.2 M ammonium acetate, 0.1 M BisTris pH 5.5, 25% PEG3350 supplemented with 20% EG as cryo in 2 steps, unique puck ID ...Details: BrovA.00232.a.B1.PS02131 at 15.8 mg/mL against MCSG1 screen condition B3 0.2 M ammonium acetate, 0.1 M BisTris pH 5.5, 25% PEG3350 supplemented with 20% EG as cryo in 2 steps, unique puck ID zxp4-1, crystal tracking ID 257586b3

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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 300 mm CCD / Detector: CCD / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→47.481 Å / Num. obs: 50090 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.263 % / Biso Wilson estimate: 54.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.077 / Χ2: 0.973 / Net I/σ(I): 15.21 / Num. measured all: 163446 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.823.2530.542.4237160.7570.64799.7
2.82-2.93.2520.4262.9936240.8280.50999.3
2.9-2.983.2630.3343.7835150.8970.499.5
2.98-3.073.260.2654.8734630.9240.31798.9
3.07-3.183.260.211633000.9510.25299.6
3.18-3.293.2540.1617.6332030.9690.19398.9
3.29-3.413.270.1249.8930980.9810.14899.1
3.41-3.553.260.09712.2929570.9880.11698.8
3.55-3.713.2670.07714.9928830.9930.09298.6
3.71-3.893.280.06317.9126830.9940.07598.7
3.89-4.13.2630.05320.5926000.9960.06398.6
4.1-4.353.280.04523.4424660.9970.05498.4
4.35-4.653.2850.0426.4722770.9970.04898.1
4.65-5.023.2610.03728.4621190.9970.04497.8
5.02-5.53.2740.03728.3119500.9970.04497.3
5.5-6.153.3030.03728.5417760.9970.04497.6
6.15-7.13.2620.03231.715660.9980.03897.5
7.1-8.73.2890.02338.7313350.9990.02896.8
8.7-12.33.2150.02144.7810160.9990.02697
12.3-47.4813.0640.02245.415430.9990.02690

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFR

3ifr


Resolution: 2.75→47.481 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2298 2062 4.12 %
Rwork0.1664 --
obs0.1691 50052 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.91 Å2 / Biso mean: 62.8348 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 2.75→47.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13968 0 0 136 14104
Biso mean---43.54 -
Num. residues----1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814305
X-RAY DIFFRACTIONf_angle_d1.0219579
X-RAY DIFFRACTIONf_chiral_restr0.0572240
X-RAY DIFFRACTIONf_plane_restr0.0082559
X-RAY DIFFRACTIONf_dihedral_angle_d14.7148334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8107X-RAY DIFFRACTION9.312TORSIONAL
12B8107X-RAY DIFFRACTION9.312TORSIONAL
13C8107X-RAY DIFFRACTION9.312TORSIONAL
14D8107X-RAY DIFFRACTION9.312TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7499-2.81390.33071330.25863230336399
2.8139-2.88420.31511410.24183212335399
2.8842-2.96220.2961340.2213197333199
2.9622-3.04940.33211260.21513250337699
3.0494-3.14780.29851330.21473163329699
3.1478-3.26030.26561470.21973236338399
3.2603-3.39080.28091290.20873195332499
3.3908-3.5450.29981440.18023197334199
3.545-3.73190.23321490.16413210335999
3.7319-3.96560.22661280.15053228335699
3.9656-4.27160.19711380.13643196333498
4.2716-4.70110.16251350.11973180331598
4.7011-5.38050.17261260.12743168329498
5.3805-6.77580.24261550.1683162331797
6.7758-47.48820.18371440.14893166331096
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)
16.9909-1.0972-0.25913.6887-0.13322.46820.21330.01850.9550.0768-0.1372-0.1294-0.7355-0.3591-0.10120.35580.10070.00040.36210.00740.359569.272212.836144.5924
24.4176-0.3640.43212.8339-0.12242.8237-0.0503-0.56560.14350.15890.0753-0.1681-0.13350.2082-0.03050.21670.0374-0.00340.44260.05040.288577.4206-1.284349.7176
31.5280.0045-0.19950.59640.37064.88610.0131-0.167-0.0868-0.07270.13490.1913-0.5128-0.2145-0.13280.23890.01170.01410.32390.04550.366762.6543-2.22933.3443
42.88280.0058-0.33292.4049-1.045.3469-0.17550.1273-0.1478-0.4160.2094-0.01970.0854-0.2278-0.06740.2721-0.0448-0.00010.2145-0.04560.314966.7033-8.428918.0612
51.7561-0.8397-0.35491.73911.90965.18510.0491-0.1725-0.1591-0.1477-0.11030.2474-0.0533-0.81480.06750.2396-0.04260.01570.40120.10310.407755.9215-4.906529.6438
60.4807-0.2412-0.55562.7506-0.55811.81230.1286-0.1306-0.09340.30890.0751.28440.5915-0.6342-0.07470.6084-0.30240.00360.84190.4261.086238.8648-45.15853.8087
70.7436-0.51011.03110.3593-0.86332.69890.28520.2566-0.39120.54240.13760.85960.7476-0.70330.08910.7658-0.53390.16051.33180.88261.283234.6011-47.922362.618
81.1663-0.2937-0.15352.5311-0.71851.9638-0.02490.06440.02940.33230.38390.4459-0.0116-0.7215-0.34550.4672-0.06790.02460.65540.28160.592248.0441-28.651752.8846
90.99220.1248-0.29490.64970.50620.5884-0.1453-0.6791-0.050.71380.47160.4949-0.0331-0.457-0.19170.6401-0.05350.03590.64360.23740.506453.7137-32.635262.4342
101.2315-0.1829-0.57461.17160.59020.5115-0.2595-0.4351-0.2585-0.00450.34190.25551.0763-0.25-0.10620.8511-0.1018-0.10410.58930.22680.505958.456-46.163850.6776
110.6014-0.0724-0.35510.0149-0.07241.23560.22480.0303-0.2765-0.0726-0.1543-0.12260.6887-0.1167-0.07530.871-0.1225-0.09980.36280.13490.512154.6471-49.769128.4062
121.0625-0.12690.74692.1267-0.3090.55650.5847-0.3878-0.29520.4418-0.291-0.12771.2673-0.2742-0.08131.2975-0.2426-0.08860.55830.18290.616656.5735-58.687440.5793
130.27730.0934-1.01720.2369-0.28624.34390.2068-0.1716-0.40140.3714-0.04010.01030.69260.1409-0.01291.0566-0.1061-0.12220.49510.23170.571959.2883-53.480141.8389
142.33681.64380.15743.1187-2.1393.07450.11460.73250.66010.05470.32480.4533-0.75280.1285-0.43681.4497-0.1205-0.03510.68370.09190.589646.51042.0284.2951
151.4520.2907-0.23992.162-0.04962.0983-0.39310.69360.3249-1.15180.40620.0001-0.4238-0.3605-0.03481.457-0.2295-0.02510.85910.10470.610247.978-1.886178.0861
162.5415-0.2919-0.57690.6813-0.91722.9291-0.19330.8295-0.1551-0.73230.21540.1632-0.0667-0.141-0.04051.1807-0.2492-0.0510.7191-0.09430.46443.2623-17.39685.4855
170.4432-0.0112-0.58790.0163-0.28354.37180.12140.3650.3837-0.98760.2906-0.1420.0293-0.1132-0.29011.2068-0.30910.09420.79010.04380.525558.1196-4.607986.5628
181.7806-0.4445-0.69440.4961-0.72062.9931-0.01950.2273-0.0227-0.56910.2573-0.2562-0.17820.308-0.23680.5925-0.20730.12970.4884-0.13240.414255.9919-8.0128110.182
194.99230.51530.65184.09260.43263.1516-0.08070.44620.0101-0.8706-0.0144-0.1079-0.88750.8750.13890.7713-0.26790.1770.7102-0.09040.465465.5976-2.1077104.1123
201.6507-0.9831-0.68131.033-0.15241.8967-0.22260.40240.0415-1.1220.4005-0.5541-0.70440.8963-0.23711.1643-0.48320.24091.0563-0.10270.666467.0728-2.27988.6977
218.7617.6719-3.58398.8492-2.55295.5827-0.40980.13390.0768-0.4530.3447-0.06490.57030.36230.00780.4509-0.02510.02920.497-0.06870.318559.3586-14.102120.1726
227.5275-3.96975.65697.2075-5.96328.5746-0.751-0.06740.348-0.28480.2322-0.2285-0.0596-0.25740.47720.7695-0.0709-0.10710.3324-0.05780.541475.8889-58.794196.5877
232.41391.16350.80392.69430.87812.2039-0.6180.4788-0.6038-0.68210.7618-0.4079-0.00470.4607-0.18680.8467-0.1820.11070.4921-0.19170.554788.5253-55.302294.0988
241.29941.0223-0.10051.49361.41393.733-0.19230.18570.0151-0.37280.1920.13210.056-0.28910.02160.6025-0.0056-0.10410.26490.01920.410279.2598-42.0828112.3633
252.2896-0.0107-1.11972.08861.0814.1939-0.0037-0.0992-0.2304-0.09020.04550.12180.0233-0.0453-0.09030.5347-0.0368-0.09590.286-0.01360.38781.4552-40.715123.0777
263.25560.00581.79020.5650.74311.9829-0.3590.01950.1395-0.6880.13590.3214-0.3822-0.25640.18720.72270.0458-0.18350.40920.0130.490671.0351-36.845109.6065
271.23570.87320.23151.61551.22464.5893-0.14510.11580.151-0.54880.28940.2883-0.8816-0.5562-0.13380.7484-0.0411-0.13240.34250.07820.466577.008-36.9301108.4835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 60 )A0 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 220 )A61 - 220
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 328 )A221 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 384 )A329 - 384
5X-RAY DIFFRACTION5chain 'A' and (resid 385 through 483 )A385 - 483
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 44 )B0 - 44
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 77 )B45 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 175 )B78 - 175
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 228 )B176 - 228
10X-RAY DIFFRACTION10chain 'B' and (resid 229 through 286 )B229 - 286
11X-RAY DIFFRACTION11chain 'B' and (resid 287 through 384 )B287 - 384
12X-RAY DIFFRACTION12chain 'B' and (resid 385 through 424 )B385 - 424
13X-RAY DIFFRACTION13chain 'B' and (resid 425 through 483 )B425 - 483
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 60 )C0 - 60
15X-RAY DIFFRACTION15chain 'C' and (resid 61 through 90 )C61 - 90
16X-RAY DIFFRACTION16chain 'C' and (resid 91 through 220 )C91 - 220
17X-RAY DIFFRACTION17chain 'C' and (resid 221 through 258 )C221 - 258
18X-RAY DIFFRACTION18chain 'C' and (resid 259 through 384 )C259 - 384
19X-RAY DIFFRACTION19chain 'C' and (resid 385 through 424 )C385 - 424
20X-RAY DIFFRACTION20chain 'C' and (resid 425 through 458 )C425 - 458
21X-RAY DIFFRACTION21chain 'C' and (resid 459 through 483 )C459 - 483
22X-RAY DIFFRACTION22chain 'D' and (resid 0 through 44 )D0 - 44
23X-RAY DIFFRACTION23chain 'D' and (resid 45 through 258 )D45 - 258
24X-RAY DIFFRACTION24chain 'D' and (resid 259 through 328 )D259 - 328
25X-RAY DIFFRACTION25chain 'D' and (resid 329 through 384 )D329 - 384
26X-RAY DIFFRACTION26chain 'D' and (resid 385 through 424 )D385 - 424
27X-RAY DIFFRACTION27chain 'D' and (resid 425 through 483 )D425 - 483

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