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- PDB-7reu: Crystal structure of Aro4p, 3-deoxy-D-arabino-heptulosonate-7-pho... -

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Basic information

Entry
Database: PDB / ID: 7reu
TitleCrystal structure of Aro4p, 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase from Candida auris, L-Tyr complex
Components3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase
KeywordsLYASE / BETA-ALPHA-BARREL / SYNTHASE / ALDOLASE / SYNTHETASE / shikimate pathway / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesCandida auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsStogios, P.J. / Evdokimova, E. / Tan, K. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of Aro4p, 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase from Candida auris, L-Tyr complex
Authors: Stogios, P.J.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 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: 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase
B: 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5248
Polymers79,8452
Non-polymers6806
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-52 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.355, 121.355, 205.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase / Aro4p


Mass: 39922.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida auris (fungus) / Gene: Aro4 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A2H0ZNV2

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 1.8 M tri-ammonum citrate, 0.1 M Tris pH 8.6, 0.5 mM TCEP cryoprotectant Paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 19301 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 64.1 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.034 / Net I/σ(I): 25.6
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 1057 / CC1/2: 0.83 / Rpim(I) all: 0.259 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OFR

1ofr


Resolution: 2.79→42.91 Å / SU ML: 0.3108 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.5238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1886 9.98 %RANDOM
Rwork0.1807 17014 --
obs0.1865 18900 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.3 Å2
Refinement stepCycle: LAST / Resolution: 2.79→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 43 61 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335497
X-RAY DIFFRACTIONf_angle_d0.5577409
X-RAY DIFFRACTIONf_chiral_restr0.0452840
X-RAY DIFFRACTIONf_plane_restr0.0039966
X-RAY DIFFRACTIONf_dihedral_angle_d20.32292081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.870.35461310.26411170X-RAY DIFFRACTION89.11
2.87-2.950.31821400.24821251X-RAY DIFFRACTION95.08
2.95-3.050.31221360.23841279X-RAY DIFFRACTION96.06
3.05-3.160.34821450.24261282X-RAY DIFFRACTION96.94
3.16-3.280.26891430.2291292X-RAY DIFFRACTION97.55
3.28-3.430.29811430.20211309X-RAY DIFFRACTION97.71
3.43-3.610.24071450.18141302X-RAY DIFFRACTION98.3
3.61-3.840.25321450.17541318X-RAY DIFFRACTION98.45
3.84-4.140.23781480.17071318X-RAY DIFFRACTION98.72
4.14-4.550.2241500.14751351X-RAY DIFFRACTION99.54
4.55-5.210.22021490.15191341X-RAY DIFFRACTION99
5.21-6.560.21021510.18861363X-RAY DIFFRACTION99.15
6.56-42.910.18711600.15951438X-RAY DIFFRACTION97.44
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)
16.927688591671.257316712872.530464829875.165999730851.183074796362.54353291078-0.6840167791591.4034477308-0.826428685405-0.09369498862630.562465558451-0.2234346308920.1189054149970.6496860679840.07452319462250.742213476677-0.0267189982169-0.0226990030690.794612639186-0.2276393996560.43572010453828.40233.17560.905
22.25306204026-0.414840588164-1.396284177682.006790387750.6073554286346.48538680102-0.110655279960.222207577272-0.184012415633-0.26128988383-0.183340252850.7840801559930.464067590211-0.6850054816240.2900367904980.455203819199-0.131681017099-0.1246502505580.637825416072-0.09744436465770.714354922162-8.47836.49670.57
32.979054914940.304099583177-0.9442139704661.44383044454-0.06334213699464.26708686554-0.0564703353250.194112473872-0.197274996215-0.05010456141630.05182325027710.0175976059790.411322952363-0.0913535337864-0.04361695961530.3083434442910.0109501703165-0.09019390636870.324063156109-0.09746029432110.4276872299154.87140.70272.692
45.137901822122.198087977990.6489375787823.40883358074-0.03429392817143.985404511470.128389706098-0.321482509748-0.570000225535-0.00143746688949-0.1355402533530.201688957480.683545750027-0.4342651807050.02719667927660.425639376085-0.0694691948788-0.01254381139290.563463709083-0.03546423480290.55359197174-8.07535.10987.425
55.01309952162-3.36109843368-4.417587299553.3992323860.6753929438728.443483894652.27406195858-4.88175620997-0.590537756167-2.223400073391.505270825412.16852819516-0.0001694095988662.24441816039-3.880639665840.77778274233-0.337124389404-0.1708776431061.02320349024-0.03296617978480.8616335601895.80146.4164.394
69.40108883836-0.842390795429-4.120900437582.025149775620.3216914739412.8789677669-0.6921843214891.469191317870.974963962512-0.09596160748270.4222527732690.1319522585450.053312620559-0.08340244283950.2511999570920.630258774834-0.102499263441-0.08796428458160.728328887535-0.0299682060550.32907183849916.76749.88459.023
74.50844665750.6403797339513.757809858955.24178264203-2.257419835427.27044096652-0.1314622275390.1848671839290.335648712685-0.0126204727462-0.002542524300430.102457040543-0.3453273239210.134685506550.09578387792220.366116707742-0.01496998164430.01812002048280.483639040907-0.1438592584690.40556054192536.82449.56475.701
83.881532547390.6390224087651.649749588281.26083825079-0.2075342126474.430933712870.08745333801030.0310772670217-0.2072133904770.1127833702120.06533172634940.06538594853180.2040240626240.0130880724285-0.1537173202160.3647217354610.0757683386673-0.06322519007580.285619386177-0.09934680456970.37109791223126.16540.90974.976
93.06265942555-0.23507389570.9718817282527.94849974719-3.186869506574.624668926090.00398494740051-0.4216203231110.170889122960.2783688585890.2102189658690.297663422242-0.1702310205830.0506012677105-0.2465291537580.4171246650970.0270290248033-0.0427610030790.451398972635-0.0903208176860.336039495236.04348.77189.553
101.99972530556-0.5155528026342.000889923460.762281531821-1.524892533287.84586514129-0.243978682853-0.3495876564590.2480789683390.09578645584910.0706449721507-0.263992652987-0.108708283871-0.133114903020.02989604878251.013037804510.410562182959-0.4892766728020.0219283114256-0.2832071375640.74636197199226.0437.66865.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:23 )A5 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:111 )A24 - 111
3X-RAY DIFFRACTION3( CHAIN A AND RESID 112:249 )A112 - 249
4X-RAY DIFFRACTION4( CHAIN A AND RESID 250:365 )A250 - 365
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:401 )A401
6X-RAY DIFFRACTION6( CHAIN B AND RESID 8:34 )B8 - 34
7X-RAY DIFFRACTION7( CHAIN B AND RESID 35:123 )B35 - 123
8X-RAY DIFFRACTION8( CHAIN B AND RESID 124:249 )B124 - 249
9X-RAY DIFFRACTION9( CHAIN B AND RESID 250:365 )B250 - 365
10X-RAY DIFFRACTION10( CHAIN B AND RESID 401:401 )B401

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