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- PDB-4knw: The crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AN... -

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Basic information

Entry
Database: PDB / ID: 4knw
TitleThe crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE
ComponentsN-acylneuraminate-9-phosphatase
KeywordsHYDROLASE / N-ACETYLNEURAMINATE / NEU5AC-9-PHOSPHATE / CARBOHYDRATE METABOLISM / N-ACETYLNEURAMINIC ACID PHOSPHATASE / NANP / HDHD4
Function / homology
Function and homology information


N-acylneuraminate-9-phosphatase / N-acetylglucosamine biosynthetic process / N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / Sialic acid metabolism / dephosphorylation / cytosol
Similarity search - Function
Haloacid dehalogenase hydrolase-like domain / HAD-superfamily hydrolase, subfamily IA, CTE7 / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / Four Helix Bundle (Hemerythrin (Met), subunit A) / HAD superfamily / HAD-like superfamily / Up-down Bundle ...Haloacid dehalogenase hydrolase-like domain / HAD-superfamily hydrolase, subfamily IA, CTE7 / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / Four Helix Bundle (Hemerythrin (Met), subunit A) / HAD superfamily / HAD-like superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / N-acylneuraminate-9-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsKlei, H.E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: Observation of extensive dynamics in an enzyme/inhibitor complex.
Authors: Kim, S.H. / Constantine, K.L. / Duke, G.J. / Goldfarb, V. / Hunt, J.T. / Johnson, S. / Kish, K. / Klei, H.E. / McDonnell, P.A. / Metzler, W.J. / Mueller, L. / Poss, M.A. / Fairchild, C.R. / Bhide, R.S.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 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 / 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_asym_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_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_asym_id / _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_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: N-acylneuraminate-9-phosphatase
B: N-acylneuraminate-9-phosphatase
C: N-acylneuraminate-9-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7919
Polymers86,3743
Non-polymers4186
Water724
1
A: N-acylneuraminate-9-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9303
Polymers28,7911
Non-polymers1392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acylneuraminate-9-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9303
Polymers28,7911
Non-polymers1392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: N-acylneuraminate-9-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9303
Polymers28,7911
Non-polymers1392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.777, 102.560, 186.665
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 N-acylneuraminate-9-phosphatase / Haloacid dehalogenase-like hydrolase domain-containing protein 4 / Neu5Ac-9-Pase


Mass: 28791.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf147, HDHD4, NANP / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8TBE9, N-acylneuraminate-9-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 500 mM postassium formate, 100 mM glycyl-glycine, pH 8.5, 20% (w/v) PEG 1500, 0.01%(w/v) N-dodecyl-b-D-maltoside, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.699→50 Å / Num. obs: 25337 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.2 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1396refinement
PDB_EXTRACT3.11data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KNV

4knv


Resolution: 2.699→35.128 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / Isotropic thermal model: RESTRAINED / σ(F): 1.33 / Phase error: 32.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2959 615 2.44 %
Rwork0.2542 --
obs0.2553 25240 98.76 %
all-25261 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5473 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2---20.75 Å20 Å2
3---18.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.699→35.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 18 4 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055340
X-RAY DIFFRACTIONf_angle_d0.7167266
X-RAY DIFFRACTIONf_dihedral_angle_d11.561834
X-RAY DIFFRACTIONf_chiral_restr0.048875
X-RAY DIFFRACTIONf_plane_restr0.003934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6995-2.9710.34521340.32085995X-RAY DIFFRACTION98
2.971-3.40060.31511610.28956136X-RAY DIFFRACTION100
3.4006-4.28320.30891650.24936158X-RAY DIFFRACTION99
4.2832-35.1310.26981550.23246336X-RAY DIFFRACTION98
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMLIGAND.TOP
X-RAY DIFFRACTION5LIGAND.PARAM

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