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- PDB-4bf5: Structure of broad spectrum racemase from Aeromonas hydrophila -

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Basic information

Entry
Database: PDB / ID: 4bf5
TitleStructure of broad spectrum racemase from Aeromonas hydrophila
ComponentsALANINE RACEMASE
KeywordsISOMERASE / D-AMINO ACIDS
Function / homology
Function and homology information


alanine metabolic process / amino-acid racemase / alanine racemase activity / periplasmic space
Similarity search - Function
Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PYRIDOXAL-5'-PHOSPHATE / Broad specificity amino-acid racemase
Similarity search - Component
Biological speciesAEROMONAS HYDROPHILA SUBSP. HYDROPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCarrasco-Lopez, C. / Hermoso, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases.
Authors: Espaillat, A. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Pietrosemoli, N. / Otero, L.H. / Alvarez, L. / De Pedro, M.A. / Pazos, F. / Davis, B.M. / Waldor, M.K. / Hermoso, J.A. / Cava, F.
History
DepositionMar 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_leaving_atom_flag / _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: ALANINE RACEMASE
B: ALANINE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,40035
Polymers91,3872
Non-polymers2,01333
Water16,772931
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-231.8 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.666, 81.850, 78.286
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALANINE RACEMASE / / BROAD SPECTRUM RACEMASE


Mass: 45693.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEROMONAS HYDROPHILA SUBSP. HYDROPHILA (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0KLG5, alanine racemase

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Non-polymers , 5 types, 964 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 931 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): PLP IS COVALENTLY LINKED TO THE LYS74

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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: 1.64 Å3/Da / Density % sol: 25.05 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.45→42.1 Å / Num. obs: 124710 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BEU

4beu


Resolution: 1.45→42.122 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 21.74 / Stereochemistry target values: ML
Details: RESIDUES A410-A417 AND B386-395 ARE DISORDERED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2079 8964 7.2 %
Rwork0.1917 --
obs0.1929 124710 99.92 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.096 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 18.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.955 Å20 Å2-0.1897 Å2
2--6.3048 Å20 Å2
3----4.3498 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 96 931 7147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046346
X-RAY DIFFRACTIONf_angle_d0.628581
X-RAY DIFFRACTIONf_dihedral_angle_d11.7992355
X-RAY DIFFRACTIONf_chiral_restr0.038944
X-RAY DIFFRACTIONf_plane_restr0.0021105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.30542780.30823763X-RAY DIFFRACTION98
1.4665-1.48370.33043000.28963855X-RAY DIFFRACTION100
1.4837-1.50180.28362790.26363846X-RAY DIFFRACTION100
1.5018-1.52080.27462980.26213839X-RAY DIFFRACTION100
1.5208-1.54090.25953010.23333846X-RAY DIFFRACTION100
1.5409-1.5620.26613110.24453851X-RAY DIFFRACTION100
1.562-1.58430.26643180.24283790X-RAY DIFFRACTION100
1.5843-1.60790.25042850.22593891X-RAY DIFFRACTION100
1.6079-1.63310.23112790.22133881X-RAY DIFFRACTION100
1.6331-1.65980.25452940.21623851X-RAY DIFFRACTION100
1.6598-1.68850.22682930.20933829X-RAY DIFFRACTION100
1.6885-1.71920.22433220.20543863X-RAY DIFFRACTION100
1.7192-1.75220.22183020.20383835X-RAY DIFFRACTION100
1.7522-1.7880.23282880.19943842X-RAY DIFFRACTION100
1.788-1.82690.23452880.19433898X-RAY DIFFRACTION100
1.8269-1.86940.21273170.19363824X-RAY DIFFRACTION100
1.8694-1.91610.22262960.1883870X-RAY DIFFRACTION100
1.9161-1.96790.21452920.18673840X-RAY DIFFRACTION100
1.9679-2.02580.20392970.17933888X-RAY DIFFRACTION100
2.0258-2.09120.19033180.1743820X-RAY DIFFRACTION100
2.0912-2.1660.19893130.17423878X-RAY DIFFRACTION100
2.166-2.25270.19812980.17293842X-RAY DIFFRACTION100
2.2527-2.35520.19943100.17513866X-RAY DIFFRACTION100
2.3552-2.47930.18632960.18183858X-RAY DIFFRACTION100
2.4793-2.63470.20512930.18793879X-RAY DIFFRACTION100
2.6347-2.8380.19813120.18723852X-RAY DIFFRACTION100
2.838-3.12360.20513200.18113861X-RAY DIFFRACTION100
3.1236-3.57530.18282940.17053914X-RAY DIFFRACTION100
3.5753-4.50370.15792930.1583899X-RAY DIFFRACTION100
4.5037-42.13990.20922790.2093975X-RAY DIFFRACTION100

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