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- PDB-1saw: X-ray structure of homo sapiens protein FLJ36880 -

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Basic information

Entry
Database: PDB / ID: 1saw
TitleX-ray structure of homo sapiens protein FLJ36880
Componentshypothetical protein FLJ36880
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Fumarylacetoacetatehydrolase family
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism / pyruvate metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Oxaloacetate tautomerase FAHD1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsManjasetty, B.A. / Niesen, F.H. / Delbrueck, H. / Goetz, F. / Sievert, V. / Buessow, K. / Behlke, J. / Heinemann, U.
CitationJournal: Biol.Chem. / Year: 2004
Title: X-ray structure of fumarylacetoacetate hydrolase family member Homo sapiens FLJ36880.
Authors: Manjasetty, B.A. / Niesen, F.H. / Delbruck, H. / Gotz, F. / Sievert, V. / Bussow, K. / Behlke, J. / Heinemann, U.
History
DepositionFeb 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein FLJ36880
B: hypothetical protein FLJ36880
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8846
Polymers49,7762
Non-polymers1084
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-49 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.792, 77.239, 114.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer generated from the dimer in the asymmetric unit.

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Components

#1: Protein hypothetical protein FLJ36880


Mass: 24887.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZP566J2046 / Plasmid: PSFEP250B074 / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1 / References: UniProt: Q6P587
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.57 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Magnesium chloride, Na HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9083 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 2003 / Details: MIRRORS
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9083 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 21466 / Num. obs: 21327 / % possible obs: 91 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 21.2
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.4 / Num. unique all: 922 / Rsym value: 0.329 / % possible all: 60.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS MODEL (PDB ENTRIES 1NR9 and 1GTT)

1nr9

1gtt


Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.13 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23876 1085 5.1 %RANDOM
Rwork0.20374 ---
obs-20279 91.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.745 Å2
Baniso -1Baniso -2Baniso -3
1-8.21 Å20 Å20 Å2
2---3.97 Å20 Å2
3----4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 4 128 3238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223184
X-RAY DIFFRACTIONr_bond_other_d0.0020.022924
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9714337
X-RAY DIFFRACTIONr_angle_other_deg0.74636818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755410
X-RAY DIFFRACTIONr_chiral_restr0.0660.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023498
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02582
X-RAY DIFFRACTIONr_nbd_refined0.1830.2637
X-RAY DIFFRACTIONr_nbd_other0.2220.23320
X-RAY DIFFRACTIONr_nbtor_other0.0830.21802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.0310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.27
X-RAY DIFFRACTIONr_mcbond_it0.3781.52065
X-RAY DIFFRACTIONr_mcangle_it0.69623327
X-RAY DIFFRACTIONr_scbond_it0.90331119
X-RAY DIFFRACTIONr_scangle_it1.5664.51010
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 56
Rwork0.295 997

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