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- PDB-2gu6: E. coli methionine aminopeptidase in complex with NleP, 1: 2, di-... -

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Basic information

Entry
Database: PDB / ID: 2gu6
TitleE. coli methionine aminopeptidase in complex with NleP, 1: 2, di-metalated
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / Mono-metalated / mononuclear / Mn(II)-form / enzyme-inhibitor complex / metalloenzyme
Function / homology
Function and homology information


initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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: 1.7 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
Water5,963331
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)49.704, 64.034, 76.347
Angle α, β, γ (deg.)90.000, 108.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / Methionyl 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 / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
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 30, 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: 1.7→20 Å / Num. all: 46683 / Num. obs: 46683 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.90.164.72550165100.1688.7
1.79-1.93.90.1156.52449662500.11589.9
1.9-2.033.90.0769.52328059450.07690.9
2.03-2.193.90.06211.72197756170.06292.2
2.19-2.43.90.05213.52044152230.05293.2
2.4-2.693.90.04814.21867147790.04894.3
2.69-3.13.90.04215.81675343000.04295.3
3.1-3.83.90.03119.91423836610.03196.3
3.8-5.383.90.03118.61109628780.03197.2
5.38-13.63.70.0411.8569415200.0492

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Phasing

Phasing MRRfactor: 0.333 / Cor.coef. Fo:Fc: 0.734
Highest resolutionLowest resolution
Rotation3 Å13.6 Å
Translation3 Å13.6 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: 1.7→13.596 Å / FOM work R set: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2302 4.6 %RANDOM
Rwork0.198 ---
all0.209 50192 --
obs0.209 46271 92.2 %-
Solvent computationBsol: 33.284 Å2
Displacement parametersBiso mean: 13.393 Å2
Baniso -1Baniso -2Baniso -3
1-1.825 Å20 Å2-0.532 Å2
2---1.674 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→13.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 26 331 4419
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.308
X-RAY DIFFRACTIONc_mcbond_it1.0241.5
X-RAY DIFFRACTIONc_scbond_it1.9932
X-RAY DIFFRACTIONc_mcangle_it1.4282
X-RAY DIFFRACTIONc_scangle_it2.9232.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 46

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.710.347470.299920967
1.71-1.730.299350.285937972
1.73-1.740.35430.292880923
1.74-1.750.255490.258901950
1.75-1.770.298430.26931974
1.77-1.780.288600.257927987
1.78-1.80.24480.222884932
1.8-1.810.283540.226928982
1.81-1.830.319410.223920961
1.83-1.840.236500.1989671017
1.84-1.860.251470.205889936
1.86-1.880.218550.186943998
1.88-1.90.237500.188894944
1.9-1.920.23510.1799551006
1.92-1.940.248500.19922972
1.94-1.960.241540.193931985
1.96-1.980.263560.2039451001
1.98-2.010.212460.199948994
2.01-2.030.191280.189941969
2.03-2.060.308460.29611007
2.06-2.080.206540.1989561010
2.08-2.110.266490.208927976
2.11-2.140.248340.1999731007
2.14-2.170.242490.2029581007
2.17-2.210.257490.2069581007
2.21-2.240.225530.2019481001
2.24-2.280.241460.2069611007
2.28-2.320.197570.1889671024
2.32-2.370.232520.1989811033
2.37-2.420.216560.192925981
2.42-2.470.19580.1929791037
2.47-2.530.259460.2039611007
2.53-2.590.249460.2079821028
2.59-2.660.178490.1949941043
2.66-2.740.275520.2129831035
2.74-2.830.248470.2069761023
2.83-2.930.203520.20910151067
2.93-3.040.266600.2059751035
3.04-3.180.202490.2079911040
3.18-3.350.217560.2039881044
3.35-3.560.22620.20410121074
3.56-3.830.224560.17710091065
3.83-4.210.156420.15810021044
4.21-4.810.142460.14710221068
4.81-6.040.189670.17410111078
6.04-200.186620.1899911053
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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