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- PDB-1pb0: YCDX PROTEIN IN AUTOINHIBITED STATE -

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Basic information

Entry
Database: PDB / ID: 1pb0
TitleYCDX PROTEIN IN AUTOINHIBITED STATE
ComponentsHypothetical protein ycdX
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-alpha-barrel / trinuclear zinc / autoinhibition
Function / homology
Function and homology information


phosphoric ester hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / bacterial-type flagellum-dependent swarming motility / phosphatase activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Probable phosphatase YcdX / : / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Probable phosphatase YcdX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTeplyakov, A. / Obmolova, G. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L.
Citation
#1: Journal: Proteins / Year: 2003
Title: Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.
Authors: Teplyakov, A. / Obmolova, G. / Khil, P.P. / Howard, A.J. / Camerini-Otero, R.D. / Gilliland, G.L.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: Hypothetical protein ycdX
B: Hypothetical protein ycdX
C: Hypothetical protein ycdX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,02622
Polymers80,7773
Non-polymers1,24919
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-326 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.130, 77.330, 82.280
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains the entire trimer that corresponds to the oligomeric state of the protein in solution

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Components

#1: Protein Hypothetical protein ycdX


Mass: 26925.529 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCDX / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P75914
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 60% AS, 3% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2003 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 59787 / Num. obs: 59787 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7470 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M65

1m65


Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.949 / SU B: 1.628 / SU ML: 0.05 / σ(F): 0 / ESU R: 0.135 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.164 --
all-59272 -
obs-59272 100 %
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: 24.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.03 Å2
2---0.78 Å20 Å2
3---1.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.135 Å
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5435 0 29 717 6181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215592
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9327581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795697
X-RAY DIFFRACTIONr_chiral_restr0.1010.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024267
X-RAY DIFFRACTIONr_nbd_refined0.2360.22814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2522
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.218
X-RAY DIFFRACTIONr_mcbond_it4.61143518
X-RAY DIFFRACTIONr_mcangle_it5.88165628
X-RAY DIFFRACTIONr_scbond_it8.08382074
X-RAY DIFFRACTIONr_scangle_it9.72491953
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.175 4188
obs-4188

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