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- PDB-6lla: Crystal structure of Providencia alcalifaciens 3-dehydroquinate s... -

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Basic information

Entry
Database: PDB / ID: 6lla
TitleCrystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+ and NAD
Components3-dehydroquinate synthase
KeywordsLYASE / Rossmann fold / Cytoplasm / Metal-binding / NAD-binding
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 3-dehydroquinate synthase
Similarity search - Component
Biological speciesProvidencia alcalifaciens F90-2004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsNeetu, N. / Katiki, M. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: J.Bacteriol. / Year: 2020
Title: Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway.
Authors: Neetu, N. / Katiki, M. / Dev, A. / Gaur, S. / Tomar, S. / Kumar, P.
History
DepositionDec 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate synthase
B: 3-dehydroquinate synthase
C: 3-dehydroquinate synthase
D: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,10752
Polymers164,4774
Non-polymers5,63048
Water19,7081094
1
A: 3-dehydroquinate synthase
C: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,28828
Polymers82,2392
Non-polymers3,04926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-dehydroquinate synthase
D: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,81924
Polymers82,2392
Non-polymers2,58122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.390, 59.920, 143.800
Angle α, β, γ (deg.)90.000, 93.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA1 - 36114 - 374
21METMETILEILEBB1 - 36114 - 374
12METMETPROPROAA1 - 36214 - 375
22METMETPROPROCC1 - 36214 - 375
13METMETPROPROAA1 - 36214 - 375
23METMETPROPRODD1 - 36214 - 375
14GLYGLYPROPROBB0 - 36213 - 375
24GLYGLYPROPROCC0 - 36213 - 375
15METMETPROPROBB1 - 36214 - 375
25METMETPROPRODD1 - 36214 - 375
16METMETILEILECC1 - 36114 - 374
26METMETILEILEDD1 - 36114 - 374

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-dehydroquinate synthase / DHQS


Mass: 41119.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia alcalifaciens F90-2004 (bacteria)
Gene: aroB, HMPREF1562_0140 / Production host: Escherichia coli (E. coli) / References: UniProt: X6Q997, 3-dehydroquinate synthase

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Non-polymers , 5 types, 1142 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM Bis Tris Propane (pH 7.0) buffer, 200 mM MgCl2 and 28% polyethylene glycol 4000
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.87→143.46 Å / Num. obs: 123349 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6118 / CC1/2: 0.81 / Rpim(I) all: 0.38 / Rrim(I) all: 0.55

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKF

3okf


Resolution: 1.88→143.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.882 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 6015 4.9 %RANDOM
Rwork0.1734 ---
obs0.1765 117334 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.54 Å2 / Biso mean: 40.942 Å2 / Biso min: 14.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20.56 Å2
2--0.35 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.88→143.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10917 0 367 1094 12378
Biso mean--43.27 47.33 -
Num. residues----1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01911520
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210958
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.99815592
X-RAY DIFFRACTIONr_angle_other_deg1.154325415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15151440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81524.798446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.891151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0011550
X-RAY DIFFRACTIONr_chiral_restr0.1280.21820
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022143
X-RAY DIFFRACTIONr_rigid_bond_restr7.942322478
X-RAY DIFFRACTIONr_sphericity_free23.245706
X-RAY DIFFRACTIONr_sphericity_bonded23.495522685
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A225780.1
12B225780.1
21A216520.12
22C216520.12
31A216900.12
32D216900.12
41B217620.12
42C217620.12
51B218620.12
52D218620.12
61C216960.12
62D216960.12
LS refinement shellResolution: 1.88→1.925 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.313 436 -
Rwork0.233 8598 -
obs--98.86 %
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)
10.00040.0001-0.00030.00160.00030.0005-0.00320.003700.00480.0045-0.00280.0037-0.004-0.00130.05790.0022-0.00360.07950.00250.01325.01295.869453.6943
20.0057-0.00310.00020.0017-00.0003-0.003-0.00190.0027-0.00050.0019-0.0015-0.0016-0.00420.00110.0573-0.00340.00090.07760.00430.01357.4319-5.328319.3851
30.0046-0.0044-0.00050.00640.00010.00060.0036-0.00180.00760.0069-0.0053-0.00770.00160.00640.00180.0464-0.0058-0.00130.0822-0.0020.0126-35.83654.720954.4844
40.00320.00140.00050.0009-0.00020.0008-0.00940.00650.0012-0.00680.0039-0.00210.00060.00760.00550.0584-0.00320.00410.08750.00790.0214-33.2367-5.44713.1546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 401
2X-RAY DIFFRACTION2B0 - 401
3X-RAY DIFFRACTION3C0 - 401
4X-RAY DIFFRACTION4D1 - 401

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