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- PDB-1vjr: Crystal structure of 4-nitrophenylphosphatase (TM1742) from Therm... -

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Basic information

Entry
Database: PDB / ID: 1vjr
TitleCrystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution
Components4-nitrophenylphosphatase
KeywordsHYDROLASE / TM1742 / 4-nitrophenylphosphatase / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


phosphatase activity / metal ion binding / cytoplasm
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / NagD protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT ...SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-nitrophenylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6844
Polymers30,5541
Non-polymers1303
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.998, 93.998, 160.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 4-nitrophenylphosphatase


Mass: 30554.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1742 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X264, EC: 3.1.3.41
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.35 Å3/Da / Density % sol: 76.82 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 2M sodium chloride, 0.1M MES pH 6.5, 0.1M sodium dihydrogen phosphate, 0.1M potassium dihydrogen phosphate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 0.9999, 0.9799
DetectorType: ADSC / Detector: CCD / Date: May 22, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.99991
30.97991
ReflectionResolution: 2.4→94 Å / Num. obs: 28916 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 57.98 Å2 / Rsym value: 0.072 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2087 / Rsym value: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
autoSHARPphasing
REFMAC5.2.0000refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→51.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.955 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.19427 1485 5.1 %RANDOM
Rwork0.16381 ---
obs0.1653 27354 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.646 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--1.56 Å20 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 3 279 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222130
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9792889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94524.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7711514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021607
X-RAY DIFFRACTIONr_nbd_refined0.1980.2989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.211
X-RAY DIFFRACTIONr_mcbond_it2.0831357
X-RAY DIFFRACTIONr_mcangle_it3.09252149
X-RAY DIFFRACTIONr_scbond_it6.4868848
X-RAY DIFFRACTIONr_scangle_it8.8511732
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 120 5.78 %
Rwork0.274 1955 -
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)
12.23990.5936-0.8812.5158-1.48123.36990.0751-0.193-0.130.0875-0.071-0.1962-0.02170.4375-0.0042-0.0568-0.03920.00730.01010.0083-0.068689.99359.64621.62
22.191-0.9504-0.35422.1412-0.05351.36530.02230.0442-0.0351-0.1267-0.0632-0.11150.11060.08740.041-0.0133-0.06750.0689-0.0301-0.0355-0.073888.25369.999-1.586
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
11-1 - 7211 - 84
21183 - 259195 - 271
3273 - 18285 - 194

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