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- PDB-3g5p: Structure and activity of human mitochondrial peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 3g5p
TitleStructure and activity of human mitochondrial peptide deformylase, a novel cancer target
ComponentsPeptide deformylase, mitochondrial
KeywordsHYDROLASE / PEPTIDE DEFORMYLASE / HUMAN / MITOCHONDRIA / Iron / Metal-binding / Mitochondrion / Protein biosynthesis / Transit peptide
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / co-translational protein modification / peptide deformylase / peptide deformylase activity / 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
: / PHOSPHATE ION / 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 / 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 / pdbx_struct_conn_angle / 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 / _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_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

Downloads & links

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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)83,60816
Polymers82,6124
Non-polymers99612
Water12,881715
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)83,60816
Polymers82,6124
Non-polymers99512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area13670 Å2
ΔGint-181 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)41,8048
Polymers41,3062
Non-polymers4986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area4840 Å2
ΔGint-80 kcal/mol
Surface area17540 Å2
MethodPISA
3
B: Peptide deformylase, mitochondrial
hetero molecules

D: Peptide deformylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8048
Polymers41,3062
Non-polymers4986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area4940 Å2
ΔGint-79 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.332, 77.825, 111.041
Angle α, β, γ (deg.)90.00, 107.93, 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 57.51 %
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: 99992 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 5.2 % / Rsym value: 0.061
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.38 / % 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→37.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.855 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18697 5136 5 %RANDOM
Rwork0.16111 ---
obs0.16241 97531 99.64 %-
all-100609 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.25 Å2
2---0.26 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 44 715 6539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0225940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.9718064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96122.394284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20315996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0891576
X-RAY DIFFRACTIONr_chiral_restr0.1960.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214580
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_it1.5081.53668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73625940
X-RAY DIFFRACTIONr_scbond_it4.1532272
X-RAY DIFFRACTIONr_scangle_it6.6724.52124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 347 -
Rwork0.213 6962 -
obs--96.17 %
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)
10.05810.02890.07430.4709-0.23180.5715-0.00910.00960.0125-0.0357-0.0169-0.004-0.05730.04470.0260.0557-0.0178-0.0170.00940.00850.017931.16114.3997.932
20.35950.30040.05130.4651-0.19640.38330.0113-0.0432-0.01550.0017-0.0052-0.00110.042-0.0581-0.0060.0439-0.0305-0.00640.03090.00050.021619.565-14.70925.407
30.7517-0.15930.08140.06720.0530.2957-0.013-0.0439-0.0415-0.0107-0.02240.033-0.0197-0.05020.03540.02310.0222-0.01260.0421-0.01510.03316.225-33.402-27.145
40.39630.1005-0.11530.20530.02580.7607-0.00690.0271-0.0253-0.03680.0254-0.0249-0.06320.0836-0.01850.03630.0007-0.00260.03280.00080.015136.943-30.644-44.456
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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