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- PDB-2gfh: Crystal structure of a n-acetylneuraminic acid phosphatase (nanp)... -

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Basic information

Entry
Database: PDB / ID: 2gfh
TitleCrystal structure of a n-acetylneuraminic acid phosphatase (nanp) from mus musculus at 1.90 A resolution
Componentshaloacid dehalogenase-like hydrolase domain containing 4
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-acylneuraminate-9-phosphatase / N-acetylglucosamine biosynthetic process / Sialic acid metabolism / N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / carbohydrate metabolic process
Similarity search - Function
Haloacid dehalogenase hydrolase-like domain / HAD-superfamily hydrolase, subfamily IA, CTE7 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / 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 / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / 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
PHOSPHATE ION / N-acylneuraminate-9-phosphatase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein C20orf147 homolog (17391249) from Mus musculus at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: haloacid dehalogenase-like hydrolase domain containing 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5205
Polymers29,3051
Non-polymers2154
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: haloacid dehalogenase-like hydrolase domain containing 4
hetero molecules

A: haloacid dehalogenase-like hydrolase domain containing 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,04110
Polymers58,6102
Non-polymers4318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3360 Å2
ΔGint-80 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.259, 71.259, 195.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein haloacid dehalogenase-like hydrolase domain containing 4


Mass: 29304.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 17391249 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CPT3

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Non-polymers , 5 types, 112 molecules

#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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.54 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 1.8M (NH4)H2PO3, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: Single crystal, cylindrically bent, asymmetrically cut Si(220) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24076 / % possible obs: 99.2 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.304 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.9-1.935.30.473.3411201.42793.8
1.93-1.9760.3711151.44596
1.97-2.016.60.32511661.46999.7
2.01-2.058.30.29411911.558100
2.05-2.098.60.24711771.518100
2.09-2.148.60.21211791.47100
2.14-2.198.60.19811841.399100
2.19-2.258.50.18211951.403100
2.25-2.328.60.13411811.30899.8
2.32-2.398.50.12611991.282100
2.39-2.488.50.11111931.353100
2.48-2.588.50.08812061.271100
2.58-2.78.50.08211961.358100
2.7-2.849.60.08112111.30899.9
2.84-3.0211.40.07312141.31699.8
3.02-3.2511.70.06112321.27499.8
3.25-3.5811.70.05312301.19499.8
3.58-4.0911.10.04512411.06399.5
4.09-5.1610.50.04612791.0599.5
5.16-5090.04513671.0796.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 1x42A

Resolution: 1.9→44.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.019 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. NA, CL, PO4, AND EDO MODELED BASED ON CRYSTALIIZATION CONDITIONS AND RELATED STRUCTURES. 3. BASED ON HOMOLOGOUS STRUCTURES, NA COULD ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. NA, CL, PO4, AND EDO MODELED BASED ON CRYSTALIIZATION CONDITIONS AND RELATED STRUCTURES. 3. BASED ON HOMOLOGOUS STRUCTURES, NA COULD ALSO BE MODELED AS MG. 4. THERE IS UNMODELED DENSITY NEAR LYS91 AND LYS243. 5. RESIDUES 63-66 ARE DISORDERED AND WERE NOT MODELED. 6. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1209 5.1 %RANDOM
Rwork0.208 ---
obs0.21 23709 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 11 108 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221931
X-RAY DIFFRACTIONr_bond_other_d0.0010.021780
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.972613
X-RAY DIFFRACTIONr_angle_other_deg0.79434127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79724.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31215342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.851513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined0.2240.2435
X-RAY DIFFRACTIONr_nbd_other0.1710.21797
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2953
X-RAY DIFFRACTIONr_nbtor_other0.0890.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2107
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0610.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.24
X-RAY DIFFRACTIONr_mcbond_it1.94631226
X-RAY DIFFRACTIONr_mcbond_other0.5813504
X-RAY DIFFRACTIONr_mcangle_it3.09351969
X-RAY DIFFRACTIONr_scbond_it5.0428723
X-RAY DIFFRACTIONr_scangle_it7.04311642
LS refinement shellResolution: 1.897→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 87 -
Rwork0.241 1532 -
obs-1619 93.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3989-0.50490.50542.5462-0.37513.15440.1476-0.10910.09690.04140.0560.1134-0.0496-0.2443-0.2036-0.13750.03470.0839-0.11150.0272-0.23686.20521.22211.852
22.871-1.20230.95343.9727-1.46694.90170.06320.24130.1186-0.6069-0.1244-0.03830.15650.24510.0613-0.02710.0872-0.02550.01080.044-0.0845-6.0629.725-14.221
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-2 - 1810 - 30
21109 - 247121 - 259
3219 - 10831 - 120

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