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- PDB-2gu5: E. coli methionine aminopeptidase in complex with NleP, 1: 1, di-... -

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Basic information

Entry
Database: PDB / ID: 2gu5
TitleE. coli methionine aminopeptidase in complex with NleP, 1: 1, di-metalated
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Mono-metalated / mononuclear / Mn(II)-form / enzyme-inhibitor complex / metalloenzyme
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / (1-AMINO-PENTYL)-PHOSPHONIC ACID / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYe, Q.Z.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis of catalysis by monometalated methionine aminopeptidase.
Authors: Ye, Q.Z. / Xie, S.X. / Ma, Z.Q. / Huang, M. / Hanzlik, R.P.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,02710
Polymers58,4272
Non-polymers6008
Water5,981332
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5145
Polymers29,2141
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5145
Polymers29,2141
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.790, 64.606, 76.354
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / MAP / Peptidase M


Mass: 29213.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map / Plasmid: pGEMEX-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NLP / (1-AMINO-PENTYL)-PHOSPHONIC ACID / NORLEUCINE PHOSPHONATE


Type: L-peptide linking / Mass: 167.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO3P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 21, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 60478 / Num. obs: 60478 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.40.243.12920086580.2497.9
1.69-1.793.50.1594.72913882930.15998.9
1.79-1.913.50.116.72777378400.1199.4
1.91-2.073.60.07310.12616173260.07399.8
2.07-2.263.60.0611.82445467710.06100
2.26-2.533.60.05412.52230961130.054100
2.53-2.923.70.036191996354200.036100
2.92-3.583.70.02427.81705945870.024100
3.58-5.063.70.02130.11332735710.021100
5.06-14.23.70.02518.8696618990.02595.3

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Phasing

Phasing MRRfactor: 0.354 / Cor.coef. Fo:Fc: 0.705
Highest resolutionLowest resolution
Rotation3 Å14.19 Å
Translation3 Å14.19 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XNZ

1xnz


Resolution: 1.6→14.194 Å / FOM work R set: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3052 5 %RANDOM
Rwork0.211 ---
all0.219 60871 --
obs0.219 60462 99.3 %-
Solvent computationBsol: 36.335 Å2
Displacement parametersBiso mean: 13.148 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å2-0.279 Å2
2---1.146 Å20 Å2
3----0.354 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 26 332 4420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.295
X-RAY DIFFRACTIONc_mcbond_it0.9781.5
X-RAY DIFFRACTIONc_scbond_it1.9742
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.6-1.610.436620.42110811143
1.61-1.620.375590.39811231182
1.62-1.630.4520.35911241176
1.63-1.650.358650.34811421207
1.65-1.660.339550.31311271182
1.66-1.670.288570.28711581215
1.67-1.680.334640.30410941158
1.68-1.70.319580.28511751233
1.7-1.710.277550.25911151170
1.71-1.720.308560.23611491205
1.72-1.740.293670.24211391206
1.74-1.750.212660.20711201186
1.75-1.770.225700.21211541224
1.77-1.790.239730.21311301203
1.79-1.80.247640.21211121176
1.8-1.820.214620.19711431205
1.82-1.840.218610.19611571218
1.84-1.860.263600.20411531213
1.86-1.880.248700.19911111181
1.88-1.90.244540.19611931247
1.9-1.920.223650.20111121177
1.92-1.940.221740.1911411215
1.94-1.960.209560.20711561212
1.96-1.990.28730.22411461219
1.99-2.020.219610.20311281189
2.02-2.040.2640.20811591223
2.04-2.070.25500.22311711221
2.07-2.10.259500.22511511201
2.1-2.140.243640.22311601224
2.14-2.170.245730.21311511224
2.17-2.210.226530.21311611214
2.21-2.250.23510.21311671218
2.25-2.290.238520.20711601212
2.29-2.340.188620.18711511213
2.34-2.390.222670.20611701237
2.39-2.440.239640.211221186
2.44-2.510.227770.19911581235
2.51-2.570.228650.21411561221
2.57-2.650.221710.21111541225
2.65-2.730.295720.22311261198
2.73-2.830.234690.21711571226
2.83-2.940.245620.22111801242
2.94-3.080.214590.22111361195
3.08-3.240.277570.21911811238
3.24-3.440.191460.21611651211
3.44-3.710.177490.18411931242
3.71-4.080.198500.16611951245
4.08-4.660.193700.15911411211
4.66-5.850.158510.17312071258
5.85-200.207450.19311551200
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein_1.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5nlp_xplor_par.paramnlp_xplor_top.top

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