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- PDB-7m92: Crystal structure of unknown function protein protein B9J08_00005... -

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Basic information

Entry
Database: PDB / ID: 7m92
TitleCrystal structure of unknown function protein protein B9J08_000055 Candida auris
ComponentsHomoserine dehydrogenase
KeywordsSTRUCTURAL GENOMICS / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / homoserine biosynthetic process / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding
Similarity search - Function
Bifunctional aspartokinase/homoserine dehydrogenase I / Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Homoserine dehydrogenase
Similarity search - Component
Biological speciesCandida auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of unknown function protein protein B9J08_000055 Candida auris
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 30, 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: Homoserine dehydrogenase
B: Homoserine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)77,2702
Polymers77,2702
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-15 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.263, 111.925, 124.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homoserine dehydrogenase / HDH


Mass: 38634.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida auris (fungus) / Gene: B9J08_000055 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H1A6V9, homoserine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium Citrate pH5.0 , 30% Jeffamine ED-2001 pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 30716 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Χ2: 0.908 / Net I/σ(I): 10.2 / Num. measured all: 187954
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.394.6113690.6580.51.1220.84989.9
2.39-2.435.30.87714420.7350.4110.9710.85594.6
2.43-2.485.70.8414980.7950.3790.9240.88198
2.48-2.5360.85915210.8020.380.9410.86499.9
2.53-2.596.30.7415140.8650.3210.8080.87599.9
2.59-2.656.30.67615220.8710.2910.7380.88999.9
2.65-2.716.30.51115170.9240.220.5570.91299.9
2.71-2.796.30.42215430.9470.1810.460.92399.9
2.79-2.876.30.31515360.9630.1360.3440.92499.9
2.87-2.966.20.25215090.9750.1090.2750.94599.6
2.96-3.075.70.20515580.9810.0930.2261.00599.9
3.07-3.196.10.17115230.9840.0750.1871.0399.9
3.19-3.336.70.13515430.990.0560.1460.93499.9
3.33-3.516.60.10815580.9930.0450.1170.97199.9
3.51-3.736.60.09315690.9910.0390.1010.961100
3.73-4.026.50.08415490.9930.0350.0910.90899.9
4.02-4.426.10.07915420.990.0350.0870.95599.7
4.42-5.066.20.07215860.990.0310.0780.83699.8
5.06-6.376.50.06916060.9930.0290.0750.711100
6.37-505.80.08317110.9880.0370.0910.91999.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SBC-Collectdata collection
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q7g

1q7g


Resolution: 2.35→48.17 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 1328 5.02 %
Rwork0.1988 25123 -
obs0.2013 26451 85.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.11 Å2 / Biso mean: 39.4614 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 2.35→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5434 0 0 252 5686
Biso mean---31.75 -
Num. residues----716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.450.2561720.2321252132439
2.45-2.560.31021050.2392003210862
2.56-2.690.33731330.24632480261377
2.69-2.860.27851760.24792884306090
2.86-3.080.29661870.2423187337499
3.08-3.390.33141550.237532463401100
3.39-3.890.23651610.186332963457100
3.89-4.890.19881690.157132973466100
4.9-48.170.18811700.167534783648100
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)
11.4895-0.12890.12422.4302-1.07131.1872-0.06460.231-0.2684-0.08720.2312-0.30490.87480.57820.10070.51270.24950.07270.215-0.01070.212917.538732.480285.5288
21.2841-0.14370.0581.1813-0.04260.9282-0.141-0.0633-0.1660.5370.05950.28880.6347-0.1416-0.01910.43270.0460.130.13390.0440.18514.266738.933688.6165
32.48030.0912-0.7151.17471.33312.30970.0450.0654-0.3432-0.52340.05390.2360.4552-0.2436-0.01090.247-0.0524-0.0110.20270.03960.1958-4.433345.275159.0363
40.93580.30090.17511.08380.32082.2559-0.05490.08570.0336-0.06970.0180.3460.149-0.34010.00630.1364-0.02310.03380.18520.02950.2809-6.526550.463272.1621
51.44980.18140.65760.79460.11722.61330.0397-0.08220.09240.1935-0.01820.0495-0.37720.0088-0.02460.19140.02180.06650.1073-0.00630.150716.437566.637101.8449
62.21990.6139-0.26622.5259-0.15171.95040.0250.53970.6397-0.1875-0.0140.2764-0.57560.01130.02650.28320.00840.03340.34540.14840.346515.418977.208372.1719
71.16880.5175-0.18681.13990.31611.9437-0.04580.22680.1007-0.08360.03350.0656-0.0545-0.2351-0.03350.08870.03430.02830.18580.00060.20129.051261.864380.7112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 51 )A2 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 172 )A52 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 215 )A173 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 359 )A216 - 359
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 150 )B2 - 150
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 304 )B151 - 304
7X-RAY DIFFRACTION7chain 'B' and (resid 305 through 359 )B305 - 359

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