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- PDB-6xgs: Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Br... -

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Basic information

Entry
Database: PDB / ID: 6xgs
TitleCrystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsBIOSYNTHETIC PROTEIN / LYASE / SSGCID / 4-hydroxy-tetrahydrodipicolinate synthase / Dihydrodipicolinate synthase / Brucella suis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesBrucella suis biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330
Authors: Abendroth, J. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: 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 / 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: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,95013
Polymers135,7074
Non-polymers1,2439
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-78 kcal/mol
Surface area37810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.650, 86.650, 142.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 0 - 293 / Label seq-ID: 21 - 314

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 33926.762 Da / Num. of mol.: 4 / Fragment: BsuA.01563.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis biovar 1 (bacteria) / Strain: 1330 / Gene: dapA, BR0646, BS1330_I0642 / Plasmid: BrsuA.01563.a.A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q8G1R0, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Qiagen JCSG Core-1 screen, f12: 40% (V/V) MPD, 100mM sodium phosphate dibasic / citric acid pH 4.2: BrsuA.01563.a.A1.PW34594; tray 231309f12, cryo, 20%EG, puck atd2-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012 / Details: Si(220)
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.643
11K, H, -L20.357
ReflectionResolution: 2.2→43.33 Å / Num. obs: 60445 / % possible obs: 99.1 % / Redundancy: 4.633 % / Biso Wilson estimate: 28.674 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.141 / Χ2: 0.898 / Net I/σ(I): 11.74 / Num. measured all: 280045 / Scaling rejects: 21
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
2.2-2.264.6260.5662.6420552452444430.8040.63998.2
2.26-2.324.7260.5182.8720504439643390.8430.58398.7
2.32-2.394.740.4163.520083429942370.8870.46998.6
2.39-2.464.7460.3674.0219441415140960.8940.41398.7
2.46-2.544.7280.324.6518824401939810.9220.3699.1
2.54-2.634.7170.2625.5618145388838470.9480.29598.9
2.63-2.734.670.2416.1517416376837290.9470.27299
2.73-2.844.7030.2087.1416884362335900.9580.23599.1
2.84-2.974.6780.178.7415979344834160.9720.19299.1
2.97-3.114.6570.13211.1315224329532690.9810.14999.2
3.11-3.284.6340.11213.1914566315831430.9850.12799.5
3.28-3.484.5190.08716.5913521301029920.9910.09899.4
3.48-3.724.5030.0720.5312383276327500.9940.0899.5
3.72-4.024.4170.05923.5811493261226020.9950.06899.6
4.02-4.44.470.05227.0610794242324150.9950.05999.7
4.4-4.924.4030.04829.089463215421490.9960.05499.8
4.92-5.684.4480.05325.568442190518980.9960.06199.6
5.68-6.964.60.05426.057484163316270.9950.06199.6
6.96-9.844.6220.03536.595764125312470.9980.0499.5
9.84-43.334.5670.03338.9530836856750.9980.03798.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4i7u as per MORDA

4i7u


Resolution: 2.2→43.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.443 / SU ML: 0.076 / SU R Cruickshank DPI: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1935 3.2 %RANDOM
Rwork0.1348 ---
obs0.1357 58503 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.14 Å2 / Biso mean: 20.617 Å2 / Biso min: 8.52 Å2
Baniso -1Baniso -2Baniso -3
1--21.39 Å2-0 Å2-0 Å2
2---21.39 Å2-0 Å2
3---42.78 Å2
Refinement stepCycle: final / Resolution: 2.2→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8786 0 77 452 9315
Biso mean--30.36 27.04 -
Num. residues----1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0139037
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178451
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.63912283
X-RAY DIFFRACTIONr_angle_other_deg1.3461.56819569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72351178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2422.194433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85151464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1311560
X-RAY DIFFRACTIONr_chiral_restr0.0760.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021787
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91780.07
12B91780.07
21A91900.07
22C91900.07
31A92060.07
32D92060.07
41B92070.07
42C92070.07
51B91790.08
52D91790.08
61C91870.08
62D91870.08
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 148 -
Rwork0.198 4273 -
all-4421 -
obs--98.18 %
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)
10.6648-0.02130.13250.42840.00320.71450.01770.07840.1267-0.0483-0.0177-0.0311-0.0960.0475-0.00010.04630.00030.00470.03140.00150.0362-5.092436.95-3.8135
20.63240.00870.30080.8101-0.12220.53320.05030.03560.0007-0.0187-0.0553-0.0291-0.01410.09620.00490.01150.0079-0.00290.0718-0.0150.006513.723210.34834.6684
30.7951-0.10150.07420.72540.14740.30460.0355-0.0153-0.0924-0.00560.01030.06650.1054-0.0402-0.04580.0546-0.0075-0.03930.03610.0120.0503-17.3507-7.405212.0599
40.463-0.0993-0.15110.7261-0.14120.60290.0056-0.08920.00060.06810.02130.0663-0.0442-0.0546-0.02690.01230.0125-0.00080.06670.00040.0482-32.550322.468715.4121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 401
2X-RAY DIFFRACTION2B0 - 501
3X-RAY DIFFRACTION3C0 - 401
4X-RAY DIFFRACTION4D0 - 401

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