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- PDB-3g5k: Structure and activity of human mitochondrial peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 3g5k
TitleStructure and activity of human mitochondrial peptide deformylase, a novel cancer target
ComponentsPeptide deformylase, mitochondrial
KeywordsHYDROLASE / PEPTIDE DEFORMYLASE / ACTINONIN / Iron / Metal-binding / Mitochondrion / Protein biosynthesis / Transit peptide
Function / homology
Function and homology information


peptidyl-methionine modification / peptide deformylase / peptide deformylase activity / : / post-translational protein modification / translation / positive regulation of cell population proliferation / mitochondrion / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACTINONIN / : / Peptide deformylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEscobar-Alvarez, S. / Goldgur, Y. / Yang, G. / Ouerfelli, O. / Li, Y. / Scheinberg, D.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
Authors: Escobar-Alvarez, S. / Goldgur, Y. / Yang, G. / Ouerfelli, O. / Li, Y. / Scheinberg, D.A.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Peptide deformylase, mitochondrial
B: Peptide deformylase, mitochondrial
C: Peptide deformylase, mitochondrial
D: Peptide deformylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,39012
Polymers82,6124
Non-polymers1,7788
Water9,962553
1
A: Peptide deformylase, mitochondrial
B: Peptide deformylase, mitochondrial
hetero molecules

C: Peptide deformylase, mitochondrial
D: Peptide deformylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,39012
Polymers82,6124
Non-polymers1,7788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area14460 Å2
ΔGint-105 kcal/mol
Surface area31270 Å2
MethodPISA
2
A: Peptide deformylase, mitochondrial
hetero molecules

C: Peptide deformylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1956
Polymers41,3062
Non-polymers8894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area5270 Å2
ΔGint-39 kcal/mol
Surface area17470 Å2
MethodPISA
3
B: Peptide deformylase, mitochondrial
hetero molecules

D: Peptide deformylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1956
Polymers41,3062
Non-polymers8894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area5300 Å2
ΔGint-43 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.144, 77.830, 110.532
Angle α, β, γ (deg.)90.00, 107.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Peptide deformylase, mitochondrial / Polypeptide deformylase


Mass: 20653.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDF, PDF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HBH1, peptide deformylase
#2: Chemical
ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antibiotic*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1 M AMMONIUM PHOSPHATE MONOBASIC, 0.1 M SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 100609 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Rsym value: 0.06
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZXZ

1zxz


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.943 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19347 5160 5 %RANDOM
Rwork0.16356 ---
obs0.16504 98055 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.14 Å2
2---0.24 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 112 553 6445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0226016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4721.9828156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03122.394284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79115996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0831576
X-RAY DIFFRACTIONr_chiral_restr0.2740.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214644
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_it1.6931.53668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.98425940
X-RAY DIFFRACTIONr_scbond_it4.52932348
X-RAY DIFFRACTIONr_scangle_it7.4654.52216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 366 -
Rwork0.223 6847 -
obs--94.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00930.0180.04720.4008-0.18630.4978-0.01640.00330.0006-0.0411-0.01160.0033-0.0610.04160.02810.097-0.0213-0.0170.01280.01010.024631.27314.4358.006
20.20650.21240.02870.3156-0.15190.35690.0016-0.03190.002-0.0184-0.0012-0.00920.0548-0.0706-0.00040.0775-0.0411-0.00980.032-0.00230.030519.655-14.625.349
30.63-0.14640.13840.06050.03530.2227-0.0244-0.0427-0.0326-0.0136-0.0210.0244-0.0365-0.06670.04540.05270.036-0.01610.0498-0.01720.03656.088-33.43-27.081
40.18920.1168-0.10080.09530.05020.7382-0.01820.0082-0.0236-0.03040.0221-0.0079-0.07650.0927-0.00390.07780.0008-0.00810.04310.00360.021236.997-30.564-44.516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 185
2X-RAY DIFFRACTION2B3 - 185
3X-RAY DIFFRACTION3C3 - 185
4X-RAY DIFFRACTION4D3 - 185

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