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- PDB-7m3k: Crystal Structure of Galactonate dehydratase from Brucella melite... -

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Basic information

Entry
Database: PDB / ID: 7m3k
TitleCrystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308
ComponentsGalactonate dehydratase
KeywordsLYASE / SSGCID / structural genomics / seattle structural genomics center for infectious disease
Function / homology
Function and homology information


galactonate dehydratase / galactonate dehydratase activity
Similarity search - Function
Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dihydroxy-acid and 6-phosphogluconate dehydratase:ATP/GTP-binding site motif A (P-loop)
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0729
Polymers66,2551
Non-polymers8178
Water4,828268
1
A: Galactonate dehydratase
hetero molecules

A: Galactonate dehydratase
hetero molecules

A: Galactonate dehydratase
hetero molecules

A: Galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,28636
Polymers265,0204
Non-polymers3,26632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+5/31
crystal symmetry operation10_666-y+1,-x+1,-z+5/31
MethodPISA
Unit cell
Length a, b, c (Å)144.950, 144.950, 167.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-1014-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Galactonate dehydratase


Mass: 66255.047 Da / Num. of mol.: 1 / Fragment: BrabA.18180.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: BAB2_0294 / Plasmid: BrabA.18180.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YJ21, galactonate dehydratase

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Non-polymers , 6 types, 276 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents JCSG+ screen, condition b10 200mM Magnesium chloride, 100mM sodium cacodylate pH 6.5, 20% (w/V) PEG 3350: BrabA.18180.a.B1.PS02071 at 27.12mg/ml: tray 256086 b10: cryo: direct: puck bvd7-1.

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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: Apr 27, 2014 / 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: 2.3→50 Å / Num. obs: 46675 / % possible obs: 99.9 % / Redundancy: 14.887 % / Biso Wilson estimate: 47.905 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.09 / Χ2: 0.92 / Net I/σ(I): 19.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.3615.4760.5854.233850.9540.604100
2.36-2.4215.3770.4735.0732970.9710.488100
2.42-2.4915.4210.3946.3232220.9770.406100
2.49-2.5715.450.3267.5931220.9830.336100
2.57-2.6615.3740.2848.8630290.9840.294100
2.66-2.7515.3730.23710.4829390.990.245100
2.75-2.8515.3060.18513.5528520.9930.191100
2.85-2.9715.2880.15116.3527370.9950.155100
2.97-3.115.1780.12419.8326410.9960.128100
3.1-3.2515.0120.10323.2925120.9980.107100
3.25-3.4314.8060.09425.724160.9980.097100
3.43-3.6414.5030.07731.0222890.9980.08100
3.64-3.8914.3190.0733.7221540.9980.072100
3.89-4.213.9890.06336.7120130.9990.06599.9
4.2-4.613.8930.05839.6318630.9990.06100
4.6-5.1413.8970.05739.3317130.9990.05999.9
5.14-5.9414.040.05538.9315070.9990.057100
5.94-7.2714.040.04840.813140.9990.049100
7.27-10.2913.550.0443.9310410.9990.041100
10.29-5011.7820.03640.66290.9990.03896.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
MR-Rosettaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-rosetta starting from PDB entry 5OYN

5oyn


Resolution: 2.3→44.24 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2037 4.37 %0
Rwork0.1804 44573 --
obs0.1816 46610 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4243 0 38 268 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554391
X-RAY DIFFRACTIONf_angle_d0.75685982
X-RAY DIFFRACTIONf_chiral_restr0.0485671
X-RAY DIFFRACTIONf_plane_restr0.0068802
X-RAY DIFFRACTIONf_dihedral_angle_d12.97521559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.29391310.23572917X-RAY DIFFRACTION99.9
2.35-2.410.24431380.2192917X-RAY DIFFRACTION99.93
2.41-2.480.22051090.1882922X-RAY DIFFRACTION99.93
2.48-2.550.20861500.18722910X-RAY DIFFRACTION99.9
2.55-2.630.21311240.18452941X-RAY DIFFRACTION100
2.63-2.730.21431360.18772929X-RAY DIFFRACTION100
2.73-2.840.21721270.19742936X-RAY DIFFRACTION100
2.84-2.970.23161560.18662931X-RAY DIFFRACTION100
2.97-3.120.21261380.18622949X-RAY DIFFRACTION100
3.12-3.320.23621250.18592968X-RAY DIFFRACTION99.97
3.32-3.570.21111290.17972981X-RAY DIFFRACTION100
3.57-3.930.20291280.16372993X-RAY DIFFRACTION99.97
3.93-4.50.17571600.14932993X-RAY DIFFRACTION99.97
4.5-5.670.16731380.16913054X-RAY DIFFRACTION99.97
5.67-44.240.23261480.19843232X-RAY DIFFRACTION99.62
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)
10.696930344875-0.219288262719-0.02906107187661.394456697260.2146125462861.63008575454-0.06902000967480.136435996284-0.193737475969-0.106857006873-0.08864889302650.2750380459150.237128774024-0.2450076395150.1248182474970.2705129704690.05080132526030.03897256326050.343749491966-0.09827232114450.34054778262332.684844844639.2815607675120.982937227
23.838937084980.2457660172031.811054477293.28029190665-0.3142370708333.046143287210.105460221305-0.502378394308-0.01936380435820.357421539285-0.1916790712171.712993404760.337737600937-0.7476000086140.07484933439930.692396260632-0.0422434268229-0.08155032911050.857042655568-0.1889480896231.2774142803810.782977229240.1216812914106.433820019
30.8827438423420.3333965588290.2900085017783.636608745030.4147707597062.50726876050.2990150478160.70880089504-0.447483207441-1.06136211558-0.2947208874040.8270039739010.276503038551-0.2277617498540.00765968271490.6387864675610.11845643926-0.224331533220.698988558971-0.2007701764590.50797968594326.385533329948.764671225797.5188094285
44.177467687390.4457422185950.02560996282993.937539281670.6962050171093.83660049013-0.1620690387790.284365434222-0.0423535612992-0.1530573447760.07814268756-0.194963370351-0.1620688990640.3331927684850.09946069790690.2549940463910.07768684774190.02757531134760.285688923469-0.009770984403060.20158287697147.033383679459.9060956304127.403177525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 102 through 403 )102 - 40392 - 393
22chain 'A' and (resid 404 through 504 )404 - 504394 - 494
33chain 'A' and (resid 505 through 597 )505 - 597495 - 587
44chain 'A' and (resid 11 through 101 )11 - 1011 - 91

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