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- PDB-5czj: Crystal structure of HypD, a 1-pyrroline-4-hydroxy-2-carboxylate ... -

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Basic information

Entry
Database: PDB / ID: 5czj
TitleCrystal structure of HypD, a 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Sinorhizobium meliloti
ComponentsDihydrodipicolinate synthase
KeywordsHYDROLASE / N-acetylneuraminate lyase sub-family / (alpha/beta)8 barrel / TIM barrel / 4-hydroxy-proline metabolism
Function / homology
Function and homology information


dihydrodipicolinate synthase / lyase activity
Similarity search - Function
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
Dihydrodipicolinate synthase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsStogios, P.J. / Xu, X. / Savchenko, A.
CitationJournal: J.Bacteriol. / Year: 2016
Title: l-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti.
Authors: Chen, S. / White, C.E. / diCenzo, G.C. / Zhang, Y. / Stogios, P.J. / Savchenko, A. / Finan, T.M.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)68,9712
Polymers68,9712
Non-polymers00
Water9,710539
1
A: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)34,4861
Polymers34,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)34,4861
Polymers34,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area24820 Å2
MethodPISA
4
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)206,9136
Polymers206,9136
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16070 Å2
ΔGint-26 kcal/mol
Surface area64690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.865, 124.865, 124.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Dihydrodipicolinate synthase


Mass: 34485.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: hypD, SM_b20259 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92WT0, EC: 3.5.4.22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5 microL of 19.5 mg/mL protein solution (including 20% (w/v) glycerol) mixed with 0.5 microL of reservoir solution (0.2 M potassium/sodium tartrate, 20% (w/v) PEG3350).

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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 RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→29.431 Å / Num. obs: 49734 / % possible obs: 100 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.88
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 19.8 % / Rmerge(I) obs: 0.583 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hmc

2hmc


Resolution: 1.92→29.431 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3382 2015 4.05 %Random selection
Rwork0.2833 ---
obs0.2855 49700 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→29.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 0 539 5364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044955
X-RAY DIFFRACTIONf_angle_d0.7376724
X-RAY DIFFRACTIONf_dihedral_angle_d11.6151784
X-RAY DIFFRACTIONf_chiral_restr0.029749
X-RAY DIFFRACTIONf_plane_restr0.003878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9880.38962030.3334709X-RAY DIFFRACTION100
1.988-2.06760.39421960.32374746X-RAY DIFFRACTION100
2.0676-2.16160.36661990.31794728X-RAY DIFFRACTION100
2.1616-2.27560.36162000.30734719X-RAY DIFFRACTION100
2.2756-2.41810.38641990.31014726X-RAY DIFFRACTION100
2.4181-2.60470.3512010.29734752X-RAY DIFFRACTION100
2.6047-2.86660.34271980.30014769X-RAY DIFFRACTION100
2.8666-3.28090.35722020.28384795X-RAY DIFFRACTION100
3.2809-4.13180.28862030.25144802X-RAY DIFFRACTION100
4.1318-29.43440.31252140.2554939X-RAY DIFFRACTION100
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)
13.67160.85730.45944.444-2.67743.13290.467-0.87740.1680.39990.2785-0.1513-0.55140.1264-0.48890.1232-0.014-0.02010.4928-0.04760.313248.748624.632171.5047
23.64291.68540.72282.45650.85841.3096-0.048-0.2066-0.0538-0.027-0.04720.24940.06980.09990.10010.17720.0197-0.00640.14850.03330.179555.961123.90672.7532
35.85680.08032.44990.6547-1.6235.9125-0.2250.04690.0064-0.04340.1130.1433-0.20440.07970.10880.1782-0.027-0.00670.1224-0.00150.204366.561533.634560.4435
44.27440.6725-2.71721.2506-0.08584.2183-0.0558-0.15850.0776-0.0676-0.03910.1560.1273-0.0980.08330.1451-0.0406-0.05060.14470.00940.218846.388431.974352.1382
52.12980.20451.64471.15311.12092.8612-0.07720.0298-0.1687-0.08310.16260.00050.18650.0058-0.06820.2175-0.06170.03960.16120.01890.183536.386232.5863.2899
62.3082-1.0411.56575.4649-0.81233.27650.0961-0.6046-0.23730.25760.3306-0.04690.6416-0.3237-0.23380.3937-0.108-0.11840.22980.1060.152469.045249.905194.1473
78.62852.9906-2.94477.4631-4.77357.5785-0.2336-0.80780.0865-1.2585-0.13790.03371.36630.8570.23770.45260.1088-0.04460.4770.03340.272974.79435.900592.6876
82.6230.41340.58841.55830.97170.62810.0152-0.0407-0.09530.14830.03390.2111-0.03680.1757-0.02960.249-0.02110.02990.19760.05020.130463.583744.934593.2482
93.91933.4356-0.2027.0156-0.9922.2513-0.1957-0.1159-0.0588-0.2919-0.0340.1008-0.12010.27880.21820.17360.038-0.03610.21590.01050.197152.636557.305985.4295
101.4613-0.74440.33651.3227-0.67371.0981-0.0401-0.14260.07320.0969-0.1197-0.1041-0.05970.11290.12170.136-0.0466-0.01910.1727-0.01010.142277.985760.487785.6544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 23:44)
2X-RAY DIFFRACTION2(chain A and resid 45:129)
3X-RAY DIFFRACTION3(chain A and resid 130:216)
4X-RAY DIFFRACTION4(chain A and resid 217:280)
5X-RAY DIFFRACTION5(chain A and resid 281:340)
6X-RAY DIFFRACTION6(chain B and resid 22:40)
7X-RAY DIFFRACTION7(chain B and resid 41:45)
8X-RAY DIFFRACTION8(chain B and resid 46:132)
9X-RAY DIFFRACTION9(chain B and resid 133:213)
10X-RAY DIFFRACTION10(chain B and resid 214:340)

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