[English] 日本語
Yorodumi
- PDB-3g5p: Structure and activity of human mitochondrial peptide deformylase... -

+
Open data


ID or keywords:

Loading...

-
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


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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more