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- PDB-4cmd: The (R)-selective transaminase from Nectria haematococca -

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Basic information

Entry
Database: PDB / ID: 4cmd
TitleThe (R)-selective transaminase from Nectria haematococca
ComponentsAMINOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


carboxylic acid biosynthetic process / catalytic activity
Similarity search - Function
: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 ...: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesNECTRIA HAEMATOCOCCA MPVI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSayer, C. / Isupov, M. / Martinez-Torres, R.J. / Richter, N. / Hailes, H.C. / Ward, J. / Littlechild, J.
CitationJournal: FEBS J. / Year: 2014
Title: The Substrate Specificity, Enantioselectivity and Structure of the (R)-Selective Amine:Pyruvate Transaminase from Nectria Haematococca.
Authors: Sayer, C. / Martinez-Torres, R.J. / Richter, N. / Isupov, M.N. / Hailes, H.C. / Littlechild, J.A. / Ward, J.M.
History
DepositionJan 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: AMINOTRANSFERASE
B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4126
Polymers72,5272
Non-polymers8854
Water19,5461085
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-10.8 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.062, 133.894, 61.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35, -0.937, -0.002), (-0.937, 0.35, 0.004), (-0.003, 0.003, -1)
Vector: 143.16023, 99.23195, 65.34525)

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Components

#1: Protein AMINOTRANSFERASE


Mass: 36263.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE BETEWEEN LYS179 AND PLP / Source: (gene. exp.) NECTRIA HAEMATOCOCCA MPVI (fungus) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: C7YVL8, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.68→29.9 Å / Num. obs: 93564 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 1.68→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WRV

1wrv


Resolution: 1.68→83.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.232 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18796 4941 5 %RANDOM
Rwork0.15814 ---
obs0.15965 93564 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--2.21 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.68→83.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 54 1085 6235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195734
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9857883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15723.46263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.142151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2351552
X-RAY DIFFRACTIONr_chiral_restr0.0960.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214394
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7634.3962717
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.677.3573429
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6965.0733017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.685→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 337 -
Rwork0.311 6535 -
obs--93.92 %

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