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

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Basic information

Entry
Database: PDB / ID: 6efx
TitleCrystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A in complex with AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / ATP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 in complex with AMPPNP
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)38,9905
Polymers38,3021
Non-polymers6884
Water3,909217
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)77,97910
Polymers76,6042
Non-polymers1,3758
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)311,91640
Polymers306,4168
Non-polymers5,50032
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 area33650 Å2
ΔGint-205 kcal/mol
Surface area87530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.340, 85.340, 187.930
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-701-

HOH

21A-706-

HOH

31A-717-

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

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Protein , 1 types, 1 molecules A

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


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

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: Optimization screen based on RigakuReagents JCSG+ screen, condition D3: 49% PEG 200, 100mM KH2PO4/Na2HPO4 pH 5.7, 100mM NaCl: CrneC.19313.a.B1.PS38377 at 15mg/ml + 2.5mM MgCl2 + 2.5mM AMPPNP: ...Details: Optimization screen based on RigakuReagents JCSG+ screen, condition D3: 49% PEG 200, 100mM KH2PO4/Na2HPO4 pH 5.7, 100mM NaCl: CrneC.19313.a.B1.PS38377 at 15mg/ml + 2.5mM MgCl2 + 2.5mM AMPPNP: cryo: 10% EG + compounds: tray 301295g1, puck HWU2-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.982 Å / Num. obs: 23914 / % possible obs: 99.9 % / Redundancy: 10.728 % / Biso Wilson estimate: 31.002 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.081 / Χ2: 1.003 / Net I/σ(I): 22.84 / Num. measured all: 256552 / Scaling rejects: 256
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
2-2.057.0460.5743.4112133172317220.8890.6299.9
2.05-2.117.7730.4524.713330171617150.9360.48599.9
2.11-2.178.6270.3696.0614062163116300.9690.39399.9
2.17-2.249.2030.3187.5614807160916090.9750.337100
2.24-2.319.780.2689.1315139155215480.9880.28399.7
2.31-2.3910.7420.2410.7416177150915060.9910.25299.8
2.39-2.4812.130.20613.3317600145214510.9930.21599.9
2.48-2.5812.1790.17814.8517209141514130.9950.18699.9
2.58-2.712.2150.16116.0816332133913370.9960.16899.9
2.7-2.8312.2090.12619.9215872130113000.9970.13299.9
2.83-2.9812.2160.11321.4415013123212290.9980.11899.8
2.98-3.1612.230.08328.1414383117811760.9990.08799.8
3.16-3.3812.1920.06634.1913472110511050.9990.069100
3.38-3.6512.1380.04945.9312514103110310.9990.051100
3.65-412.0970.03953.961161396096010.041100
4-4.4711.9650.03462.111045787587410.03599.9
4.47-5.1611.9230.03263.23926477777710.033100
5.16-6.3211.7350.04252.8178746716710.9990.044100
6.32-8.9411.3920.02962.46607253353310.031100
8.94-46.9829.8750.02172.8322933632710.02397.3

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Processing

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

Resolution: 2→46.982 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1921 8.04 %0
Rwork0.1637 ---
obs0.1675 23905 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.17 Å2 / Biso mean: 29.4625 Å2 / Biso min: 5.2 Å2
Refinement stepCycle: final / Resolution: 2→46.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 41 221 2802
Biso mean--34.39 38.26 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d02706
X-RAY DIFFRACTIONf_angle_d0.933693
X-RAY DIFFRACTIONf_dihedral_angle_d161651
X-RAY DIFFRACTIONf_chiral_restr0.06413
X-RAY DIFFRACTIONf_plane_restr0494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.28191430.197715141657
2.05-2.10550.23661400.176315481688
2.1055-2.16740.24541470.161715211668
2.1674-2.23740.21421160.163615701686
2.2374-2.31730.21591260.158215561682
2.3173-2.41010.19221430.161615291672
2.4101-2.51980.24571410.16215631704
2.5198-2.65270.20121260.164115641690
2.6527-2.81880.22641310.167415531684
2.8188-3.03640.21531500.173215671717
3.0364-3.34190.24011310.167415721703
3.3419-3.82530.20231420.149416021744
3.8253-4.81870.16041340.14516141748
4.8187-46.99540.21171510.181617111862
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)
10.95530.32860.40741.03170.54591.64650.02120.0465-0.0171-0.11910.02890.0194-0.13330.0872-0.07780.1653-0.02210.01640.14880.02570.1658-29.6269-27.6349-23.8417
23.1967-0.33971.25821.9175-0.61453.8602-0.01090.54360.2255-0.69570.04330.0586-0.2799-0.01020.01720.2782-0.04140.01860.25020.05760.1676-27.0249-25.0388-37.4678
33.6006-0.09511.13931.1132-0.48982.9867-0.150.78830.1463-0.15340.089-0.1478-0.29830.71110.02120.2543-0.07520.05550.3810.01780.2059-15.1467-26.8724-34.1684
43.46611.6146-0.52432.4733-0.47171.60550.03870.02310.09170.07290.0153-0.366-0.14390.4972-0.02150.1655-0.0088-0.00230.3235-0.01390.2695-5.9239-28.8707-18.6639
51.0734-0.23460.04085.1277-0.38590.82310.0340.01370.22560.1-0.0325-0.2406-0.20290.09170.00050.1236-0.0180.00730.1444-0.00510.1531-21.3204-23.6512-15.3454
60.48780.67610.92245.31656.05086.7746-0.1213-0.08340.0930.1053-0.01670.3214-0.1223-0.1450.16340.14640.0011-0.01330.15130.0170.17-28.1088-28.95-8.3867
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 117 )A91 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 180 )A118 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 249 )A181 - 249
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 316 )A250 - 316
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 346 )A317 - 346

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