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- PDB-6efw: Crystal structure of a YjeF family protein from Cryptococcus neof... -

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Basic information

Entry
Database: PDB / ID: 6efw
TitleCrystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A
ComponentsATP-dependent (S)-NAD(P)H-hydrate dehydratase
KeywordsLYASE / SSGCID / Cryptococcus neoformans / ATP / YjeF / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ATP-dependent NAD(P)H-hydrate dehydratase / ATP-dependent NAD(P)H-hydrate dehydratase activity / metabolite repair / nicotinamide nucleotide metabolic process / ATP binding / cytoplasm
Similarity search - Function
ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / NAD(P)H-hydrate dehydratase / YjeF C-terminal domain profile. / Ribokinase-like
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent (S)-NAD(P)H-hydrate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4203
Polymers38,3021
Non-polymers1182
Water3,945219
1
A: ATP-dependent (S)-NAD(P)H-hydrate dehydratase
hetero molecules

A: ATP-dependent (S)-NAD(P)H-hydrate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8406
Polymers76,6042
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1,x,z1
2
A: ATP-dependent (S)-NAD(P)H-hydrate dehydratase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)307,36024
Polymers306,4168
Non-polymers94416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area22090 Å2
ΔGint-111 kcal/mol
Surface area92930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.420, 85.420, 187.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21A-579-

HOH

DetailsPer size exclusion chromatography the protein appears to be a dimer. However, PISA describes a very convincing crystallographic octamer. With these conflicting pieces of information the actual oligomeric structure remains unclear.

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Components

#1: Protein ATP-dependent (S)-NAD(P)H-hydrate dehydratase / ATP-dependent NAD(P)HX dehydratase / CrneC.19313.a.B1


Mass: 38301.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05097
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VIT7, ATP-dependent NAD(P)H-hydrate dehydratase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: Optimization screen based on RigakuReagents JCSG+ screen, condition A3: 40% PEG 200, 100mM KH2PO4/Na2HPO4 pH 6.1, 200mM NaCl; CrneC.19313.a.B1.PS38377 at 15mg/ml; cryo: direct; tray 302563a3, puck VLL3-1

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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: Aug 2, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→36.98 Å / Num. obs: 27708 / % possible obs: 99.8 % / Redundancy: 11.693 % / Biso Wilson estimate: 33.281 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.063 / Χ2: 1.026 / Net I/σ(I): 26.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.958.8840.5384.2919880.9220.57198.5
1.95-210.9940.4096.5219440.9670.429100
2-2.0612.2020.3148.5619260.9850.328100
2.06-2.1212.2040.24511.0518560.9890.256100
2.12-2.1912.2090.20412.8518170.9940.213100
2.19-2.2712.2060.16215.6517340.9960.16999.9
2.27-2.3611.9870.13817.8716790.9970.144100
2.36-2.4512.1560.11421.1416510.9970.119100
2.45-2.5612.0360.09724.1215400.9980.10199.9
2.56-2.6912.1290.08327.0715110.9980.087100
2.69-2.8312.1030.06832.7214380.9990.071100
2.83-312.1130.0636.1413500.9980.062100
3-3.2111.9960.05142.4612830.9990.05399.9
3.21-3.4711.7810.04747.1712020.9990.049100
3.47-3.811.8280.04253.8611040.9990.044100
3.8-4.2511.7360.03956.7510180.9990.041100
4.25-4.9111.6730.03859.518990.9990.0499.9
4.91-6.0111.6080.03357.5977310.035100
6.01-8.511.2160.02557.962510.026100
8.5-36.989.770.02257.0937010.02397.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted structure from Robetta server

Resolution: 1.9→36.98 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2015 7.27 %0
Rwork0.1631 ---
obs0.1661 27700 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.22 Å2 / Biso mean: 31.2387 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 1.9→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 6 220 2790
Biso mean--60.8 40.13 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d02727
X-RAY DIFFRACTIONf_angle_d0.913724
X-RAY DIFFRACTIONf_dihedral_angle_d15.71688
X-RAY DIFFRACTIONf_chiral_restr0.06420
X-RAY DIFFRACTIONf_plane_restr0489
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 (%)
1.9001-1.94760.2541210.18721785190698
1.9476-2.00020.2681440.179717941938100
2.0002-2.05910.22351430.167318061949100
2.0591-2.12550.21551440.162818061950100
2.1255-2.20150.20831250.16118181943100
2.2015-2.28960.20691510.15918081959100
2.2896-2.39380.2131430.16318141957100
2.3938-2.520.21751240.165618691993100
2.52-2.67780.2111590.171417871946100
2.6778-2.88450.23941390.176118521991100
2.8845-3.17470.2051600.175918261986100
3.1747-3.63370.19171330.158418581991100
3.6337-4.57670.16961600.140318822042100
4.5767-36.98680.20691690.169119802149100
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)
10.77161.01330.65661.65011.42882.27180.00440.0409-0.0192-0.13790.03460.0224-0.12610.067-0.04580.187-0.00050.01130.16480.02170.1909-29.2667-27.5516-23.4024
22.5166-0.33760.01153.6020.42494.8847-0.18150.57090.1154-0.75280.2197-0.1494-0.29420.0669-0.01870.2801-0.09030.04080.27030.03180.1978-24.4989-25.4983-38.6494
35.3901-1.17250.32852.8521-0.22034.1719-0.0680.65170.1554-0.25520.0805-0.1655-0.31280.3942-0.04130.2259-0.06930.0320.2842-0.00620.1826-12.9784-27.4391-31.993
43.47461.4824-0.6352.7101-0.96312.17130.0328-0.00080.05040.0979-0.0286-0.4126-0.13130.41830.0040.16960.0109-0.00170.2665-0.0080.266-5.4576-28.7807-18.6763
53.0693-0.88-0.66575.93181.80882.72610.1231-0.04760.3793-0.0027-0.0706-0.0291-0.3344-0.0151-0.02560.1665-0.01460.01360.16240.0030.1529-23.192-16.5464-17.3535
62.39921.933-0.79187.8291-1.96681.51240.0527-0.02190.15550.1262-0.0565-0.121-0.0460.1199-0.00240.12450.01560.00190.1492-0.00510.142-19.0194-31.2303-12.9152
70.45050.89060.98775.93076.4336.9343-0.029-0.09860.10690.2888-0.15860.45640.0173-0.23680.24180.19640.00390.00480.16280.0080.194-28.0885-29.0021-8.2806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 90 )A0 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 133 )A91 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 180 )A134 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 249 )A181 - 249
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 283 )A250 - 283
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 316 )A284 - 316
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 346 )A317 - 346

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