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- PDB-3s5n: Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase -

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Basic information

Entry
Database: PDB / ID: 3s5n
TitleCrystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase
Components4-hydroxy-2-oxoglutarate aldolase, mitochondrial
KeywordsLYASE / aldolase / beta barrel / hydroxyproline metabolism
Function / homology
Function and homology information


4-hydroxyproline catabolic process / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxalate metabolic process / glyoxylate metabolic process / N-acetylneuraminate lyase activity / pyruvate biosynthetic process / Glyoxylate metabolism and glycine degradation / glyoxylate catabolic process ...4-hydroxyproline catabolic process / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxalate metabolic process / glyoxylate metabolic process / N-acetylneuraminate lyase activity / pyruvate biosynthetic process / Glyoxylate metabolism and glycine degradation / glyoxylate catabolic process / N-acetylneuraminate catabolic process / mitochondrial matrix / protein homodimerization activity / mitochondrion
Similarity search - Function
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
: / 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsRiedel, T.J. / Lowther, W.T.
CitationJournal: Plos One / Year: 2011
Title: Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria.
Authors: Riedel, T.J. / Johnson, L.C. / Knight, J. / Hantgan, R.R. / Holmes, R.P. / Lowther, W.T.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0889
Polymers32,6531
Non-polymers4348
Water84747
1
A: 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
hetero molecules

A: 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
hetero molecules

A: 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
hetero molecules

A: 4-hydroxy-2-oxoglutarate aldolase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,35236
Polymers130,6144
Non-polymers1,73832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area15620 Å2
ΔGint-28 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.143, 142.143, 108.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein 4-hydroxy-2-oxoglutarate aldolase, mitochondrial / Dihydrodipicolinate synthase-like / DHDPS-like protein / 2-keto-4-hydroxyglutarate aldolase / KHG- ...Dihydrodipicolinate synthase-like / DHDPS-like protein / 2-keto-4-hydroxyglutarate aldolase / KHG-aldolase / Protein 569272


Mass: 32653.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf65, DHDPSL, HOGA1 / Plasmid: pET151 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86XE5, 4-hydroxy-2-oxoglutarate aldolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, KSCN, Bis tris Propane, TCEP, Ethelyene glycol, pH 8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.5 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→59.38 Å / Num. obs: 22814 / % possible obs: 100 % / Redundancy: 41.3 % / Net I/σ(I): 28.3
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 11.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.6 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.48 Å
Translation2.5 Å49.48 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.1phasing
REFMAC5.5.0063refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.524 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.657 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.232 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1170 5.1 %RANDOM
Rwork0.212 ---
obs0.2136 22814 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.8 Å2 / Biso mean: 42.4164 Å2 / Biso min: 27.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 26 47 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222298
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.973112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78523.58792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1071515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211730
X-RAY DIFFRACTIONr_mcbond_it0.5861.51464
X-RAY DIFFRACTIONr_mcangle_it1.16422354
X-RAY DIFFRACTIONr_scbond_it2.033834
X-RAY DIFFRACTIONr_scangle_it3.4234.5758
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 88 -
Rwork0.308 1571 -
all-1659 -
obs--100 %

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