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- PDB-2w4m: The Crystal Structure of human N-acetylneuraminic acid phosphatas... -

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Basic information

Entry
Database: PDB / ID: 2w4m
TitleThe Crystal Structure of human N-acetylneuraminic acid phosphatase, NANP
ComponentsN-ACYLNEURAMINATE-9-PHOSPHATASE
KeywordsHYDROLASE / N-ACETYLNEURAMINATE / NEU5AC-9- PHOSPHATE / CARBOHYDRATE METABOLISM / N-ACETYLNEURAMINIC ACID PHOSPHATASE / NANP / HDHD4 / MAGNESIUM / SIALIC ACID
Function / homology
Function and homology information


N-acylneuraminate-9-phosphatase / N-acylneuraminate-9-phosphatase activity / N-acetylglucosamine biosynthetic process / N-acetylneuraminate biosynthetic process / CMP-N-acetylneuraminate biosynthetic process / glycosylation / Sialic acid metabolism / 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 / HAD superfamily / HAD-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...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 / HAD superfamily / HAD-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / N-acylneuraminate-9-phosphatase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUgochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: The Crystal Structure of Human N-Acetylneuraminic Acid Phosphatase, Nanp
Authors: Ugochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionNov 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACYLNEURAMINATE-9-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6906
Polymers30,4061
Non-polymers2845
Water1,58588
1
A: N-ACYLNEURAMINATE-9-PHOSPHATASE
hetero molecules

A: N-ACYLNEURAMINATE-9-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,37912
Polymers60,8122
Non-polymers56810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2160 Å2
ΔGint-22.7 kcal/mol
Surface area28510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)122.740, 122.740, 74.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein N-ACYLNEURAMINATE-9-PHOSPHATASE / NEU5AC-9-PASE / HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING PROTEIN 4 / NANP


Mass: 30405.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q8TBE9, N-acylneuraminate-9-phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 5.33 Å3/Da / Density % sol: 76.95 % / Description: NONE
Crystal growTemperature: 293 K
Details: 0.8M NA_PHOSPHATE_(NA_H2_PO4)-4M, 0.16M K_PHOSPHATE_(K2_H_PO4)-4M AT 20 DEGREES C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.6→35.37 Å / Num. obs: 92013 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GFH

2gfh


Resolution: 2.6→35.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 12.328 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1043 5.2 %RANDOM
Rwork0.182 ---
obs0.184 19188 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.26 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å21.1 Å20 Å2
2--2.2 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 13 88 2052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221997
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9742705
X-RAY DIFFRACTIONr_angle_other_deg0.88133283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07124.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83415359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1151511
X-RAY DIFFRACTIONr_chiral_restr0.080.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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_it1.84831245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33652007
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3778752
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.61611697
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.372 73
Rwork0.327 1416
Refinement TLS params.Method: refined / Origin x: -55.6777 Å / Origin y: 25.4355 Å / Origin z: 7.0787 Å
111213212223313233
T0.1381 Å20.0007 Å20.0521 Å2-0.0946 Å20.0114 Å2--0.0401 Å2
L1.66 °20.5354 °20.2234 °2-4.0651 °2-0.1264 °2--2.2404 °2
S-0.0161 Å °-0.0099 Å °-0.0771 Å °-0.1543 Å °-0.0148 Å °-0.2937 Å °0.2998 Å °0.1142 Å °0.0309 Å °

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