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- PDB-4mf4: Crystal structure of a HpcH/Hpal aldolase/citrate lyase family pr... -

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Basic information

Entry
Database: PDB / ID: 4mf4
TitleCrystal structure of a HpcH/Hpal aldolase/citrate lyase family protein from Burkholderia cenocepacia J2315
ComponentsHpcH/HpaI aldolase/citrate lyase family protein
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / aldolase / citrate lyase
Function / homology
Function and homology information


aldehyde-lyase activity / cytoplasm
Similarity search - Function
: / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
HpcH/HpaI aldolase/citrate lyase family protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a HpcH/Hpal aldolase/citrate lyase family protein from Burkholderia cenocepacia J2315
Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HpcH/HpaI aldolase/citrate lyase family protein
B: HpcH/HpaI aldolase/citrate lyase family protein
C: HpcH/HpaI aldolase/citrate lyase family protein
D: HpcH/HpaI aldolase/citrate lyase family protein
E: HpcH/HpaI aldolase/citrate lyase family protein
F: HpcH/HpaI aldolase/citrate lyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,18911
Polymers173,8796
Non-polymers3105
Water17,421967
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25390 Å2
ΔGint-120 kcal/mol
Surface area49790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.110, 116.480, 161.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HpcH/HpaI aldolase/citrate lyase family protein


Mass: 28979.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: BceJ2315_04740, BCAL0476 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E7W8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: JCSG+a9: 20% PEG3350, 0.2M AmCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 95233 / Num. obs: 95110 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.15 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.15 / Num. unique all: 6950 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DXE

1dxe


Resolution: 2→48.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.517 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21254 4765 5 %RANDOM
Rwork0.16457 ---
obs0.16702 90266 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20 Å2
2---0.68 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11468 0 20 967 12455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211322
X-RAY DIFFRACTIONr_angle_refined_deg1.561.95916233
X-RAY DIFFRACTIONr_angle_other_deg0.855325856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58551584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2322.321504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.354151762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.43915133
X-RAY DIFFRACTIONr_chiral_restr0.0880.21850
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022726
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2741.7826288
X-RAY DIFFRACTIONr_mcbond_other1.2731.7826287
X-RAY DIFFRACTIONr_mcangle_it1.9862.6627888
X-RAY DIFFRACTIONr_mcangle_other1.9862.6627889
X-RAY DIFFRACTIONr_scbond_it1.9362.0455599
X-RAY DIFFRACTIONr_scbond_other1.9352.0455599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.042.9738346
X-RAY DIFFRACTIONr_long_range_B_refined4.97615.25313944
X-RAY DIFFRACTIONr_long_range_B_other4.97615.25413945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 377 -
Rwork0.199 6554 -
obs--99.99 %
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)
10.0553-0.03840.12660.2727-0.05720.2990.0004-0.0138-0.0049-0.01030.02180.0174-0.0047-0.0333-0.02220.0070.00620.00280.01080.00670.0395-23.507713.0104-31.3678
20.23850.1276-0.02340.1019-0.02770.1049-0.02760.0347-0.0248-0.00180.0072-0.0080.0104-0.00270.02040.0123-0.00750.00450.0098-0.00780.031-16.8515-20.8578-31.1857
30.1489-0.1357-0.10.17710.09510.2310.0116-0.0041-0.0114-0.0459-0.0181-0.0232-0.0559-0.00690.00660.03470.01120.01590.00810.01250.02426.2671.5069-43.3759
40.3914-0.0022-0.0550.0511-0.04170.12080.019-0.0541-0.0191-0.0139-0.0337-0.01740.01540.00750.01480.00880.0025-0.0050.03780.0170.029216.0622-13.7192-7.7487
50.1540.15710.04340.3281-0.11760.2181-0.0008-0.00250.01230.06560.00060.027-0.0497-0.01590.00020.03140.0010.01060.0146-0.00160.0073-14.4806-4.6874.8868
60.1898-0.19440.12390.36280.0710.3201-0.009-0.01790.02630.01430.0244-0.0529-0.0009-0.0037-0.01550.0186-0.0093-0.00520.0106-0.00970.03237.052519.4056-6.595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 261
2X-RAY DIFFRACTION2B4 - 261
3X-RAY DIFFRACTION3C4 - 261
4X-RAY DIFFRACTION4D4 - 261
5X-RAY DIFFRACTION5E5 - 261
6X-RAY DIFFRACTION6F5 - 261

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