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- PDB-2hxg: Crystal Structure of Mn2+ bound ECAI -

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Basic information

Entry
Database: PDB / ID: 2hxg
TitleCrystal Structure of Mn2+ bound ECAI
ComponentsL-arabinose isomerase
KeywordsISOMERASE / T2031 / NYSGXRC / tagatose production / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / arabinose catabolic process / manganese ion binding / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #10940 / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-arabinose isomerase / L-arabinose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsManjasetty, B.A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Young.Investig. / Year: 2007
Title: Crystal Structure of Mn2+-bound Escherichia coli L-arabinose Isomerase (ECAI) and Implications in Protein Catalytic Mechanism and Thermo-Stability.
Authors: Zhu, W. / Chance, M.R. / Manjasetty, B.A.
History
DepositionAug 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 12, 2014Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE ACCORDING TO THE UNP REFERENCE SEQUENCE, RESIDUE 72 IS ARG. THIS CONFLICTS WITH THE ... SEQUENCE ACCORDING TO THE UNP REFERENCE SEQUENCE, RESIDUE 72 IS ARG. THIS CONFLICTS WITH THE AUTHORS' COORDINATES, IN WHICH RESIDUE 72 IS PRO. THE AUTHORS' RESIDUE IS CONSISTENT WITH PREVIOUS CITATIONS: LEE ET AL., (1986) GENE; YURA ET AL., (1992) NUCLEIC ACIDS RES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,4946
Polymers168,3293
Non-polymers1653
Water1,856103
1
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules

A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,98812
Polymers336,6586
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area40110 Å2
ΔGint-231 kcal/mol
Surface area96680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.870, 116.870, 215.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein L-arabinose isomerase / ECAI


Mass: 56109.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: araA / Plasmid: PLASMID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q8FL89, UniProt: P08202*PLUS, L-arabinose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Tri-sodium citrate dihydrate, MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9786 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 80763 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 18.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3 / Rsym value: 0.533 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AJT

2ajt


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 47.255 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28811 1988 5.1 %RANDOM
Rwork0.22878 ---
obs0.2318 37213 92.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.798 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å22.66 Å20 Å2
2--5.31 Å20 Å2
3----7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11459 0 3 103 11565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111739
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210345
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.93115952
X-RAY DIFFRACTIONr_angle_other_deg0.783323960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0951491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5724.438543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86151837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311556
X-RAY DIFFRACTIONr_chiral_restr0.0660.21744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022401
X-RAY DIFFRACTIONr_nbd_refined0.2260.22947
X-RAY DIFFRACTIONr_nbd_other0.1920.211248
X-RAY DIFFRACTIONr_nbtor_refined0.1820.25673
X-RAY DIFFRACTIONr_nbtor_other0.0870.26510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0830.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.57552
X-RAY DIFFRACTIONr_mcbond_other0.0521.53051
X-RAY DIFFRACTIONr_mcangle_it0.541211780
X-RAY DIFFRACTIONr_scbond_it0.7234763
X-RAY DIFFRACTIONr_scangle_it1.1364.54172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 154 -
Rwork0.343 2617 -
obs--91.21 %

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