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- PDB-1rmq: Crystal structure of AphA class B acid phosphatase/phosphotransfe... -

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Basic information

Entry
Database: PDB / ID: 1rmq
TitleCrystal structure of AphA class B acid phosphatase/phosphotransferase with osmiate mimicking the catalytic intermediate
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme / osmiate
Function / homology
Function and homology information


L-phosphoserine phosphatase activity / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / magnesium ion binding / metal ion binding / identical protein binding
Similarity search - Function
HAD-superfamily phosphatase, subfamily IIIB, AphA / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / OSMIUM ION / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCalderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S.
Citation
Journal: To be Published
Title: Insights in the catalytic mechanism of AphA from Escherichia coli
Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S.
#1: Journal: FEMS Microbiol.Lett. / Year: 1997
Title: Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product
Authors: Thaller, M.C. / Schippa, S. / Bonci, A. / Cresti, S. / Rossolini, G.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray characterization of the class B acid phosphatase (AphA) from Escherichia coli
Authors: Forleo, C. / Benvenuti, M. / Calderone, V. / Schippa, S. / Docquier, J.D. / Thaller, M.C. / M Rossolini, G. / Mangani, S.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9898
Polymers47,1112
Non-polymers8796
Water5,332296
1
A: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules

A: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,97916
Polymers94,2214
Non-polymers1,75812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13870 Å2
ΔGint-165 kcal/mol
Surface area32980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.732, 66.447, 91.523
Angle α, β, γ (deg.)90.00, 121.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-540-

HOH

DetailsThe biological assembly is a tetramer, but there is a dimer in the asymmetric unit.

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Components

#1: Protein Class B acid phosphatase


Mass: 23555.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: APHA, NAPA, B4055, SF4149, S3580 / Plasmid: pATac / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Os
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.59 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM osmiate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.13980, 1.14057, 1.13800
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2002 / Details: Double crystal monochromator
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.13981
21.140571
31.1381
ReflectionResolution: 2→30.58 Å / Num. all: 31710 / Num. obs: 31710 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.344 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4531 / Rsym value: 0.402 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8N

1n8n


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.04 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23002 2265 7.1 %RANDOM
Rwork0.18325 ---
all0.18661 29421 --
obs0.18661 29421 99.25 %-
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: 26.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.58 Å2
2--0.05 Å20 Å2
3---0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.113 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 6 296 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213353
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9294548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2025415
X-RAY DIFFRACTIONr_chiral_restr0.1480.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022616
X-RAY DIFFRACTIONr_nbd_refined0.2220.21640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2284
X-RAY DIFFRACTIONr_metal_ion_refined0.3240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.228
X-RAY DIFFRACTIONr_mcbond_it1.1351.52082
X-RAY DIFFRACTIONr_mcangle_it1.85323365
X-RAY DIFFRACTIONr_scbond_it3.31631271
X-RAY DIFFRACTIONr_scangle_it5.0664.51183
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 163
Rwork0.239 2101

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