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- PDB-5cr5: X-RAY CRYSTAL STRUCTURE AT 1.61A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 5cr5
TitleX-RAY CRYSTAL STRUCTURE AT 1.61A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIPHENYL PYRROLIDINE ETHER COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / FOLD TYPE IV
Function / homology
Function and homology information


regulation of hormone levels / branched-chain-amino-acid transaminase activity / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / 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
Chem-EL1 / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.61 Å
AuthorsSomers, D.O.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library.
Authors: Deng, H. / Zhou, J. / Sundersingh, F.S. / Summerfield, J. / Somers, D. / Messer, J.A. / Satz, A.L. / Ancellin, N. / Arico-Muendel, C.C. / Sargent Bedard, K.L. / Beljean, A. / Belyanskaya, S. ...Authors: Deng, H. / Zhou, J. / Sundersingh, F.S. / Summerfield, J. / Somers, D. / Messer, J.A. / Satz, A.L. / Ancellin, N. / Arico-Muendel, C.C. / Sargent Bedard, K.L. / Beljean, A. / Belyanskaya, S.L. / Bingham, R. / Smith, S.E. / Boursier, E. / Carter, P. / Centrella, P.A. / Clark, M.A. / Chung, C.W. / Davie, C.P. / Delorey, J.L. / Ding, Y. / Franklin, G.J. / Grady, L.C. / Herry, K. / Hobbs, C. / Kollmann, C.S. / Morgan, B.A. / Pothier Kaushansky, L.J. / Zhou, Q.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase, mitochondrial
B: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,62415
Polymers83,4512
Non-polymers2,17313
Water19,4921082
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-61 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.550, 105.590, 107.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCAT(m) / Placental protein 18 / PP18


Mass: 41725.391 Da / Num. of mol.: 2 / Fragment: UNP residues 28-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Plasmid: pET-28A / Production host: Escherichia coli (E. coli)
References: UniProt: O15382, branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 1095 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-EL1 / 3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide


Mass: 578.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24BrN3O5S2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MDL Morpheus screen condition B2, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2013
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→33.81 Å / Num. obs: 101131 / % possible obs: 97.4 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Net I/σ(I): 17.4 / Num. measured all: 695861 / Scaling rejects: 288
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.635.80.7912.22229938320.6940.34376
8.78-33.816.10.02745.440936700.9980.01292.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
MOSFLM7.0.9data reduction
RefinementResolution: 1.61→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.958 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19882 5024 5 %RANDOM
Rwork0.16838 ---
obs0.1699 95729 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.621 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0 Å2
2--0.41 Å2-0 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 130 1082 6944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196147
X-RAY DIFFRACTIONr_bond_other_d0.0010.025930
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9678355
X-RAY DIFFRACTIONr_angle_other_deg0.741313624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6025739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41823.258267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.889151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3651546
X-RAY DIFFRACTIONr_chiral_restr0.0790.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021440
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_it1.6912.8892929
X-RAY DIFFRACTIONr_mcbond_other1.692.8892928
X-RAY DIFFRACTIONr_mcangle_it2.5694.8613677
X-RAY DIFFRACTIONr_mcangle_other2.5694.8613678
X-RAY DIFFRACTIONr_scbond_it2.2733.2143218
X-RAY DIFFRACTIONr_scbond_other2.2733.2153219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5915.2554679
X-RAY DIFFRACTIONr_long_range_B_refined6.16315.0378121
X-RAY DIFFRACTIONr_long_range_B_other5.67614.0837429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 377 -
Rwork0.299 6783 -
obs--95.84 %

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