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- PDB-1z9t: CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA C... -

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Basic information

Entry
Database: PDB / ID: 1z9t
TitleCRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI AT 1.54 A RESOLUTION
ComponentsHypothetical UPF0124 protein yfiH
KeywordsOXIDOREDUCTASE / PUTATIVE LACCASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / purine-nucleoside phosphorylase activity ...Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / purine-nucleoside phosphorylase activity / outer membrane-bounded periplasmic space / copper ion binding / protein homodimerization activity / cytosol
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Purine nucleoside phosphorylase YfiH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Hypothetical UPF0124 protein yfiH (np_417084.1) from Escherichia coli K12 at 1.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0124 protein yfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,62822
Polymers28,0641
Non-polymers1,56421
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.711, 80.711, 90.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical UPF0124 protein yfiH


Mass: 28064.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yfiH / Production host: Escherichia coli (E. coli) / References: UniProt: P33644
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.47 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 0.2M (NH4)2HCitrate, 20.0% PEG-3350, No Buffer pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.983967
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2005
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(311) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983967 Å / Relative weight: 1
ReflectionResolution: 1.54→60.3 Å / Num. obs: 44917 / % possible obs: 100 % / Redundancy: 6.8 % / Rsym value: 0.079 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsRsym valueDiffraction-ID
1.54-1.581007132590.7581
1.58-1.6210071.331810.5881
1.62-1.6710071.630900.4921
1.67-1.7210071.930120.4131
1.72-1.7810072.329270.3331
1.78-1.841007328500.2581
1.84-1.9110073.727150.1991
1.91-1.991006.94.226490.1661
1.99-2.081006.95.525420.1281
2.08-2.181006.97.124350.1021
2.18-2.31006.87.323130.0911
2.3-2.431006.89.122090.0761
2.43-2.61006.810.220790.0661
2.6-2.811006.810.219220.0641
2.81-3.081006.610.717980.0581
3.08-3.441006.311.216260.0531
3.44-3.9899.95.811.914580.0491
3.98-4.871006.914.912580.0371
4.87-6.891006.819.99950.031
6.89-60.398.65.9185990.031

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u05

1u05


Resolution: 1.54→60.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.087 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MASS SPEC ANALYSIS SHOWED THAT THE SE-METHIONINE INCORPATION RATE WAS ONLY 63% AND THE MODEL IS BUILT WITH THE OCCUPANCY OF THE SE ATOMS IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MASS SPEC ANALYSIS SHOWED THAT THE SE-METHIONINE INCORPATION RATE WAS ONLY 63% AND THE MODEL IS BUILT WITH THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES AT 0.75 OCCUPANCY TO ACCOUNT FOR THE REDUCED SCATTERING POWER FROM THE 37% S-MET RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2262 5 %RANDOM
Rwork0.142 ---
all0.143 ---
obs0.14324 42591 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.54→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 102 218 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221935
X-RAY DIFFRACTIONr_bond_other_d0.0010.021767
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9732597
X-RAY DIFFRACTIONr_angle_other_deg1.44734077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24923.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75515274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.241513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined0.2110.2366
X-RAY DIFFRACTIONr_nbd_other0.1890.21801
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2945
X-RAY DIFFRACTIONr_nbtor_other0.0860.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.222
X-RAY DIFFRACTIONr_mcbond_it2.00431261
X-RAY DIFFRACTIONr_mcbond_other0.4743491
X-RAY DIFFRACTIONr_mcangle_it2.43751901
X-RAY DIFFRACTIONr_scbond_it4.3588816
X-RAY DIFFRACTIONr_scangle_it6.19311695
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 178 -
Rwork0.209 3082 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.7438 Å / Origin y: 20.0477 Å / Origin z: 2.7803 Å
111213212223313233
T-0.0599 Å2-0.0136 Å20.0089 Å2--0.0317 Å2-0.0228 Å2---0.008 Å2
L1.0029 °2-0.3494 °2-0.3517 °2-0.4629 °20.2194 °2--0.6086 °2
S-0.0343 Å °0.0688 Å °-0.001 Å °-0.0294 Å °-0.0136 Å °0.02 Å °-0.0013 Å °-0.0449 Å °0.0478 Å °
Refinement TLS groupSelection: ALL

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