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- PDB-7kf3: Crystal structure of GDP-mannose 4,6-dehydratase from Brucella ab... -

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Basic information

Entry
Database: PDB / ID: 7kf3
TitleCrystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose
ComponentsGDP-mannose 4,6-dehydratase
KeywordsLYASE / SSGCID / Structural genomics / GDP-mannose 4 / 6-dehydratase / gmd / Brucella abortus / Guanosine-diphosphate-rhamnose / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / NADP+ binding
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-mannose 4,6-dehydratase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: GDP-mannose 4,6-dehydratase
B: GDP-mannose 4,6-dehydratase
C: GDP-mannose 4,6-dehydratase
D: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,33712
Polymers168,0064
Non-polymers5,3318
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25110 Å2
ΔGint-124 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 93.300, 93.770
Angle α, β, γ (deg.)89.060, 78.910, 87.510
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 202 or resid 204...
21(chain B and (resid 1 through 124 or (resid 125...
31(chain C and (resid 1 through 123 or (resid 124...
41(chain D and (resid 1 through 123 or (resid 124...

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
11METMETTHRTHR(chain A and (resid 1 through 202 or resid 204...AA1 - 2021 - 202
12ALAALAGLYGLY(chain A and (resid 1 through 202 or resid 204...AA204 - 254204 - 254
13LYSLYSLYSLYS(chain A and (resid 1 through 202 or resid 204...AA255255
14METMETNAPNAP(chain A and (resid 1 through 202 or resid 204...AA - F1 - 4011
15METMETNAPNAP(chain A and (resid 1 through 202 or resid 204...AA - F1 - 4011
16METMETNAPNAP(chain A and (resid 1 through 202 or resid 204...AA - F1 - 4011
17METMETNAPNAP(chain A and (resid 1 through 202 or resid 204...AA - F1 - 4011
21METMETLYSLYS(chain B and (resid 1 through 124 or (resid 125...BB1 - 1241 - 124
22GLNGLNGLNGLN(chain B and (resid 1 through 124 or (resid 125...BB125125
23METMETNAPNAP(chain B and (resid 1 through 124 or (resid 125...BB - H1 - 4011
24METMETNAPNAP(chain B and (resid 1 through 124 or (resid 125...BB - H1 - 4011
25METMETNAPNAP(chain B and (resid 1 through 124 or (resid 125...BB - H1 - 4011
26METMETNAPNAP(chain B and (resid 1 through 124 or (resid 125...BB - H1 - 4011
31METMETGLUGLU(chain C and (resid 1 through 123 or (resid 124...CC1 - 1231 - 123
32LYSLYSGLNGLN(chain C and (resid 1 through 123 or (resid 124...CC124 - 125124 - 125
33METMETNAPNAP(chain C and (resid 1 through 123 or (resid 124...CC - J1 - 4011
34METMETNAPNAP(chain C and (resid 1 through 123 or (resid 124...CC - J1 - 4011
35METMETNAPNAP(chain C and (resid 1 through 123 or (resid 124...CC - J1 - 4011
36METMETNAPNAP(chain C and (resid 1 through 123 or (resid 124...CC - J1 - 4011
41METMETGLUGLU(chain D and (resid 1 through 123 or (resid 124...DD1 - 1231 - 123
42LYSLYSGLNGLN(chain D and (resid 1 through 123 or (resid 124...DD124 - 125124 - 125
43METMETNAPNAP(chain D and (resid 1 through 123 or (resid 124...DD - L1 - 4011
44METMETNAPNAP(chain D and (resid 1 through 123 or (resid 124...DD - L1 - 4011
45METMETNAPNAP(chain D and (resid 1 through 123 or (resid 124...DD - L1 - 4011
46METMETNAPNAP(chain D and (resid 1 through 123 or (resid 124...DD - L1 - 4011

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Components

#1: Protein
GDP-mannose 4,6-dehydratase / GDP-D-mannose dehydratase


Mass: 42001.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: gmd, BAB1_0545 / Plasmid: Braba.00085.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YMP3, GDP-mannose 4,6-dehydratase
#2: Chemical
ChemComp-GDR / GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE


Type: RNA linking / Mass: 589.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.2 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3- ...Details: Microlytic Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma base pH 8.5: Braba.00085.a.AE1.PW38674 at 29.4mg/ml: tray 311690 d12: cryo: direct: puck zdr6-4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→48.35 Å / Num. obs: 78643 / % possible obs: 96.1 % / Redundancy: 2.198 % / Biso Wilson estimate: 49.532 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.064 / Χ2: 0.933 / Net I/σ(I): 12.13 / Num. measured all: 172882 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.412.2110.4182.0112775601057780.8080.56296.1
2.41-2.482.2130.3592.3312652592157180.8460.48396.6
2.48-2.552.2070.2693.1212031569554510.8920.36295.7
2.55-2.632.2130.2233.7211882558853680.9340.396.1
2.63-2.712.2090.194.411541542752240.9490.25596.3
2.71-2.812.2040.1485.5111108524550390.9660.296.1
2.81-2.912.2090.1166.8710692503148410.9780.15596.2
2.91-3.032.2110.0928.510346485046790.9880.12496.5
3.03-3.172.20.07310.339830464544680.9910.09996.2
3.17-3.322.1990.05613.159383446842670.9940.07695.5
3.32-3.52.1970.04416.68970425240830.9950.0696
3.5-3.722.1860.03718.928451400438660.9970.0596.6
3.72-3.972.1860.03221.977829373035810.9970.04396
3.97-4.292.1820.02825.127380350833820.9970.03796.4
4.29-4.72.1830.02527.096799322431140.9980.03496.6
4.7-5.252.1740.02527.376078290427960.9980.03396.3
5.25-6.072.1750.02726.015343255224560.9970.03696.2
6.07-7.432.170.02628.064550219520970.9970.03595.5
7.43-10.512.1730.02231.533466166815950.9980.02995.6
10.51-48.352.1140.0232.5317769168400.9980.02891.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZH

5uzh


Resolution: 2.35→48.35 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 1973 2.51 %0
Rwork0.1743 76627 --
obs0.1751 78600 96.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.43 Å2 / Biso mean: 47.4039 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 2.35→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11350 0 344 570 12264
Biso mean--36.94 44.89 -
Num. residues----1448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512025
X-RAY DIFFRACTIONf_angle_d0.74716412
X-RAY DIFFRACTIONf_dihedral_angle_d14.3314494
X-RAY DIFFRACTIONf_chiral_restr0.0461818
X-RAY DIFFRACTIONf_plane_restr0.0062223
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7112X-RAY DIFFRACTION5.685TORSIONAL
12B7112X-RAY DIFFRACTION5.685TORSIONAL
13C7112X-RAY DIFFRACTION5.685TORSIONAL
14D7112X-RAY DIFFRACTION5.685TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.410.33361650.28345387555296
2.41-2.470.27431350.25025553568897
2.47-2.550.26041430.22135405554895
2.55-2.630.26661470.21415463561096
2.63-2.720.26781770.21795463564096
2.72-2.830.25831580.2055493565196
2.83-2.960.2821380.2055501563996
2.96-3.120.25741350.20125493562897
3.12-3.310.23031130.19655454556796
3.31-3.570.22831200.17035489560996
3.57-3.930.16461520.15815506565897
3.93-4.490.17371260.13495486561296
4.49-5.660.16871340.14265494562896
5.66-48.350.17231300.15815440557095
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)
11.8842-0.4752-0.43852.01360.79331.79510.0224-0.0451-0.3750.0726-0.01890.02290.7491-0.06090.05590.7196-0.0493-0.07870.27230.01510.4641-8.9479-42.595258.8978
20.59330.24760.27961.84280.6151.88480.00190.1104-0.2890.11060.1722-0.24660.9640.2149-0.11350.78130.1084-0.09870.31090.02150.5952-0.715-45.489660.2543
31.93380.5156-0.92740.9286-0.44694.3584-0.10150.4405-0.2749-0.42550.2365-0.2520.5844-0.3011-0.08960.9455-0.0159-0.08250.4656-0.10840.6723-9.5427-42.730240.8181
42.9645-1.0063-0.08392.56820.06713.2488-0.1187-0.20410.22420.08060.2324-0.4409-0.73310.7343-0.05950.3078-0.0851-0.02370.3903-0.05440.40189.79822.194277.6132
50.57230.13410.1171.21440.08832.2580.0685-0.1652-0.08090.23720.0144-0.23260.15640.1793-0.07030.27350.0216-0.0540.33960.01620.34971.294-14.551476.5782
63.03030.1603-0.87091.74720.56332.77520.0715-0.18920.2143-0.007-0.06550.1701-0.4721-0.15260.00410.52370.028-0.02380.4961-0.03480.2932-10.7105-0.284296.4376
72.67720.4995-0.38391.83970.58452.12870.0646-0.1181-0.20260.5050.0918-0.48830.27330.5064-0.14550.42090.0908-0.17170.48160.02320.4229.248-15.014188.6276
80.9919-0.8271-0.3751.46130.36294.336-0.0454-0.50680.17230.5492-0.03890.3516-0.3391-0.29170.13630.5816-0.00930.08960.6779-0.06590.4071-16.235-2.253103.7826
92.3959-0.36710.07921.64370.72322.7139-0.2386-0.4553-0.16480.79050.1659-0.27480.28910.10250.06730.63070.0144-0.11890.49540.07520.37411.4626-16.931293.3216
102.4012-1.27510.98395.628-0.92591.9707-0.3827-0.27540.63360.58710.2463-0.4108-0.9415-0.20710.09480.68230.0416-0.02030.51-0.09980.4071-4.236811.040994.8418
112.3831.00470.9122.74990.07211.7314-0.0809-0.48510.45990.328-0.02490.2101-0.4822-0.41320.08590.42530.14970.01720.4306-0.06820.3301-18.436110.456175.8462
120.82850.41810.23611.4660.45731.954-0.1130.00890.3107-0.16470.05190.0285-0.7281-0.01960.05920.54030.0434-0.01260.23820.01390.379-8.339216.20459.7572
132.4989-0.91732.00472.0385-0.61664.5993-0.2583-0.50410.321-0.01910.1753-0.4626-0.1401-0.0740.13550.8818-0.11710.00680.5075-0.13880.64990.898723.857880.5136
142.45981.02380.60671.9136-0.69443.12470.02370.3599-0.4186-0.34480.135-0.37650.45780.3313-0.14030.30640.02440.06260.3349-0.08240.41211.5502-21.897540.0053
150.6197-0.00680.15951.63180.04092.5608-0.06140.14930.0268-0.35850.1303-0.1246-0.23150.0407-0.06920.3186-0.01850.0350.29460.0040.3057-4.695-4.568343.8816
162.33140.54111.05231.46150.76572.0926-0.06630.2726-0.0563-0.31420.04120.1015-0.1124-0.18920.03790.4835-0.0185-0.02440.44180.02680.2679-18.688-10.527328.2566
171.45510.7285-1.05392.8917-1.19422.1839-0.30050.2442-0.3608-0.16210.2780.04990.7611-0.45360.04950.7281-0.0715-0.06710.5582-0.08550.4292-18.6923-29.629829.4669
181.76-0.795-1.20013.51630.20951.9308-0.0310.2836-0.3577-0.3859-0.03510.45910.5232-0.68730.06070.3788-0.1533-0.05030.4951-0.01290.3789-24.6648-27.822952.375
191.03920.02170.89892.67160.38282.85240.0438-0.1505-0.07670.0606-0.00540.10090.2575-0.3201-0.03430.2072-0.0328-0.01030.26710.01570.2547-15.8196-19.482962.7579
200.85440.1779-0.40531.7960.56542.59850.1669-0.1474-0.16630.3272-0.1291-0.04370.5819-0.2704-0.02230.4308-0.0818-0.03580.26650.05320.3814-12.7741-29.430470.84
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 197 through 270 )B197 - 270
2X-RAY DIFFRACTION2chain 'B' and (resid 271 through 328 )B271 - 328
3X-RAY DIFFRACTION3chain 'B' and (resid 329 through 362 )B329 - 362
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 67 )C1 - 67
5X-RAY DIFFRACTION5chain 'C' and (resid 68 through 196 )C68 - 196
6X-RAY DIFFRACTION6chain 'C' and (resid 197 through 229 )C197 - 229
7X-RAY DIFFRACTION7chain 'C' and (resid 230 through 258 )C230 - 258
8X-RAY DIFFRACTION8chain 'C' and (resid 259 through 301 )C259 - 301
9X-RAY DIFFRACTION9chain 'C' and (resid 302 through 328 )C302 - 328
10X-RAY DIFFRACTION10chain 'C' and (resid 329 through 362 )C329 - 362
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 67 )D1 - 67
12X-RAY DIFFRACTION12chain 'D' and (resid 68 through 328 )D68 - 328
13X-RAY DIFFRACTION13chain 'D' and (resid 329 through 362 )D329 - 362
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 67 )A1 - 67
15X-RAY DIFFRACTION15chain 'A' and (resid 68 through 196 )A68 - 196
16X-RAY DIFFRACTION16chain 'A' and (resid 197 through 328 )A197 - 328
17X-RAY DIFFRACTION17chain 'A' and (resid 329 through 362 )A329 - 362
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 67 )B1 - 67
19X-RAY DIFFRACTION19chain 'B' and (resid 68 through 119 )B68 - 119
20X-RAY DIFFRACTION20chain 'B' and (resid 120 through 196 )B120 - 196

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