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- PDB-1m68: YCDX PROTEIN, TRINUCLEAR ZINC SITE -

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Basic information

Entry
Database: PDB / ID: 1m68
TitleYCDX PROTEIN, TRINUCLEAR ZINC SITE
ComponentsHypothetical protein ycdX
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-alpha-barrel / trinuclear zinc
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
Probable phosphatase YcdX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTeplyakov, A. / Obmolova, G. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / 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
DepositionJul 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3146
Polymers26,9261
Non-polymers3885
Water3,387188
1
A: Hypothetical protein ycdX
hetero molecules

A: Hypothetical protein ycdX
hetero molecules

A: Hypothetical protein ycdX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,94218
Polymers80,7773
Non-polymers1,16515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5890 Å2
ΔGint-485 kcal/mol
Surface area25850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.350, 77.350, 80.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe protein forms a trimer in solution that sits on the 3-fold crystal axis

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Components

#1: Protein Hypothetical protein ycdX


Mass: 26925.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P75914
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 60% AS, 5 mM Zinc Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris1reservoirpH8.5
260 %ammonium sulfate1reservoir
33 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12703 / Num. obs: 12596 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.7
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12.8 / Num. unique all: 757 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CCP4model building
REFMAC5refinement
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1M65

1m65


Resolution: 2.3→10 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.372 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.217 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 607 4.9 %RANDOM
Rwork0.16181 ---
all0.16505 11839 --
obs0.16505 11839 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: 38.198 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.92 Å20 Å2
2---1.84 Å20 Å2
3---2.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 13 188 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211859
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9322525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8793232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2115318
X-RAY DIFFRACTIONr_chiral_restr0.110.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021424
X-RAY DIFFRACTIONr_nbd_refined0.2440.3892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.512
X-RAY DIFFRACTIONr_mcbond_it5.29331166
X-RAY DIFFRACTIONr_mcangle_it8.16381875
X-RAY DIFFRACTIONr_scbond_it12.0798693
X-RAY DIFFRACTIONr_scangle_it14.0428650
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 52
Rwork0.161 824
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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