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- PDB-1rkq: Crystal structure of HAD-like phosphatase yidA from E. coli -

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Basic information

Entry
Database: PDB / ID: 1rkq
TitleCrystal structure of HAD-like phosphatase yidA from E. coli
ComponentsHypothetical protein yidAHypothesis
Keywordsstructural genomics / unknown function / Two domain structure with beta-alpha sandwich. Stucture contains a Magnesium Ion. / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sugar-phosphatase / sugar-phosphatase activity / phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Hypothetical cof family signature 2. / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Hypothetical cof family signature 2. / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar phosphatase YidA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single Crystal SIRAS by RIP / Resolution: 1.4 Å
AuthorsRamagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of NYSGRC target T1436: A Hypothetical protein yidA.
Authors: Ramagopal, U.A. / Almo, S.C.
History
DepositionNov 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yidA
B: Hypothetical protein yidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2806
Polymers62,1612
Non-polymers1204
Water11,133618
1
A: Hypothetical protein yidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1403
Polymers31,0801
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1403
Polymers31,0801
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.120, 54.871, 67.725
Angle α, β, γ (deg.)112.58, 96.37, 106.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hypothetical protein yidA / Hypothesis


Mass: 31080.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIDA, B3697, C4619, SF3767, S4004 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Y5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.31 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Magnesium Chloride,, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.97901
SYNCHROTRONNSLS X9A21.0083
Detector
TypeIDDetectorDate
MARRESEARCH1CCDAug 6, 2003
MARRESEARCH2CCDAug 6, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
21.00831
ReflectionResolution: 1.4→24 Å / Num. all: 106331 / Num. obs: 106331 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.064 / Net I/σ(I): 30.9
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.58 / Num. unique all: 10374 / Rsym value: 0.56 / % possible all: 93.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building
RESOLVEmodel building
ARP/wARPmodel building
REFMACrefinement
RESOLVEphasing
RefinementMethod to determine structure: Single Crystal SIRAS by RIP
Starting model: Experimental Phasing by single crystal SIRAS (Radiation damage).

Resolution: 1.4→24.5 Å / SU B: 1.104 / SU ML: 0.044 / Isotropic thermal model: ISOTROPIC / Cross valid method: Throught / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.068 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5253 -RANDOM
Rwork0.177 ---
all0.185 99828 --
obs-99828 95.5 %-
Refinement stepCycle: LAST / Resolution: 1.4→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 10 612 4830
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONp_bond_d0.0242820.02
X-RAY DIFFRACTIONp_angle_d0.03458160.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0414100.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0315400.04
X-RAY DIFFRACTIONp_chiral_restr0.1390.15
X-RAY DIFFRACTIONp_singtor_nbd0.16815560.3
X-RAY DIFFRACTIONp_multtor_nbd0.26926390.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.105990.3
X-RAY DIFFRACTIONp_planar_tor6.25597
X-RAY DIFFRACTIONp_staggered_tor13.41515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.25420
X-RAY DIFFRACTIONp_special_tor0015
LS refinement shellResolution: 1.4→1.469 Å
RfactorNum. reflection
Rfree0.259 660
Rwork0.2 -
obs-13179

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