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- PDB-3qz6: The crystal structure of HpcH/HpaI aldolase from Desulfitobacteri... -

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Basic information

Entry
Database: PDB / ID: 3qz6
TitleThe crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / cytoplasmic
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
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsTan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2
Authors: Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1562
Polymers29,0901
Non-polymers651
Water4,360242
1
A: HpcH/HpaI aldolase
hetero molecules

A: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3114
Polymers58,1812
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4320 Å2
ΔGint-163 kcal/mol
Surface area21460 Å2
MethodPISA
2
A: HpcH/HpaI aldolase
hetero molecules

A: HpcH/HpaI aldolase
hetero molecules

A: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4676
Polymers87,2713
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5730 Å2
ΔGint-9 kcal/mol
Surface area32640 Å2
MethodPISA
3
A: HpcH/HpaI aldolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)174,93412
Polymers174,5426
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area29220 Å2
ΔGint-518 kcal/mol
Surface area48120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.531, 131.531, 176.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-259-

ZN

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Components

#1: Protein HpcH/HpaI aldolase


Mass: 29090.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: Dhaf_2073 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B8FRX2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium citrate, 0.1M Tris.HCl, 15% (v/v) PEG400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. all: 39752 / Num. obs: 39752 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.773 / Net I/σ(I): 16
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 0.773 / Num. unique all: 1931 / Rsym value: 0.016 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.999→43.828 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1725 1906 5.03 %random
Rwork0.1523 ---
all0.1533 37911 --
obs0.1533 37911 95.34 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.947 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9299 Å2-0 Å2-0 Å2
2--1.9299 Å20 Å2
3----3.8598 Å2
Refinement stepCycle: LAST / Resolution: 1.999→43.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 1 242 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072051
X-RAY DIFFRACTIONf_angle_d0.9822781
X-RAY DIFFRACTIONf_dihedral_angle_d13.349748
X-RAY DIFFRACTIONf_chiral_restr0.065312
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.07090.24841510.22973192X-RAY DIFFRACTION86
2.0709-2.15380.24751770.20543359X-RAY DIFFRACTION89
2.1538-2.25190.20831640.17143465X-RAY DIFFRACTION93
2.2519-2.37060.19131780.15473557X-RAY DIFFRACTION95
2.3706-2.51910.1721800.14883618X-RAY DIFFRACTION96
2.5191-2.71360.16621970.15573673X-RAY DIFFRACTION97
2.7136-2.98660.18012340.15583668X-RAY DIFFRACTION98
2.9866-3.41860.17822240.15253743X-RAY DIFFRACTION100
3.4186-4.30650.13792050.13343795X-RAY DIFFRACTION100
4.3065-43.83880.15691960.13793935X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.2071 Å / Origin y: 11.587 Å / Origin z: 17.1328 Å
111213212223313233
T0.1349 Å2-0.0394 Å2-0.0372 Å2-0.1694 Å2-0.0117 Å2--0.1404 Å2
L0.4137 °20.0618 °2-0.0983 °2-0.3022 °20.177 °2--0.4876 °2
S-0.0016 Å °-0.1274 Å °0.0362 Å °0.0273 Å °0.0065 Å °-0.073 Å °-0.0698 Å °0.1775 Å °-0.0136 Å °
Refinement TLS groupSelection details: chain A

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