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- PDB-4a5p: Structure of the Shigella flexneri MxiA protein -

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Basic information

Entry
Database: PDB / ID: 4a5p
TitleStructure of the Shigella flexneri MxiA protein
ComponentsPROTEIN MXIA
KeywordsPROTEIN TRANSPORT / TYPE THREE SECRETION / EXPORT APPARATUS / NONAMER
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsAbrusci, P. / Vegara-Irigaray, M. / Johnson, S. / Roversi, P. / Friede, M.E. / Deane, J.E. / Tang, C.M. / Lea, S.M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Architecture of the major component of the type III secretion system export apparatus.
Authors: Abrusci, P. / Vergara-Irigaray, M. / Johnson, S. / Beeby, M.D. / Hendrixson, D.R. / Roversi, P. / Friede, M.E. / Deane, J.E. / Jensen, G.J. / Tang, C.M. / Lea, S.M.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Architecture of the Major Component of the Type III Secretion System Export Apparatus.
Authors: Abrusci, P. / Vergara-Irigaray, M. / Johnson, S. / Beeby, M.D. / Hendrixson, D.R. / Roversi, P. / Friede, M.E. / Deane, J.E. / Jensen, G.J. / Tang, C.M. / Lea, S.M.
History
DepositionOct 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN MXIA
B: PROTEIN MXIA
C: PROTEIN MXIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3505
Polymers132,2263
Non-polymers1242
Water28816
1
A: PROTEIN MXIA
B: PROTEIN MXIA
C: PROTEIN MXIA
hetero molecules

A: PROTEIN MXIA
B: PROTEIN MXIA
C: PROTEIN MXIA
hetero molecules

A: PROTEIN MXIA
B: PROTEIN MXIA
C: PROTEIN MXIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,04915
Polymers396,6779
Non-polymers3726
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
MethodPISA
2
A: PROTEIN MXIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1372
Polymers44,0751
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: PROTEIN MXIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1372
Polymers44,0751
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: PROTEIN MXIA


Theoretical massNumber of molelcules
Total (without water)44,0751
Polymers44,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.610, 160.610, 100.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.762, -0.647, 0.003), (0.647, 0.762, 0.004), (-0.005, -0.001, 1)-0.34974, 0.1248, -0.19259
2given(0.173, -0.985, -0.001), (0.985, 0.173, 0.002), (-0.002, -0.001, 1)-0.04535, 0.13853, -0.05213

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Components

#1: Protein PROTEIN MXIA / PROTEIN VIRH


Mass: 44075.211 Da / Num. of mol.: 3 / Fragment: CYTOPLASMIC GLOBULAR DOMAIN, RESIDUES 318-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: 5A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0A1I5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.83 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M SODIUM HEPES PH 7.5, 10% (W/V) PEG 8000, 8% ETHYLENE GLYCOL 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.15→81.5 Å / Num. obs: 23949 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 86.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 3.15→3.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2XDSdata reduction
xia2SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X4A

2x4a


Resolution: 3.15→35.72 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.8707 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.431
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1226 5.12 %RANDOM
Rwork0.2306 ---
obs0.2317 23949 93.43 %-
Displacement parametersBiso mean: 76.68 Å2
Baniso -1Baniso -2Baniso -3
1--5.3613 Å20 Å20 Å2
2---5.3613 Å20 Å2
3---10.7227 Å2
Refine analyzeLuzzati coordinate error obs: 0.699 Å
Refinement stepCycle: LAST / Resolution: 3.15→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 8 16 7414
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087495HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8810105HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3469SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes205HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1037HARMONIC5
X-RAY DIFFRACTIONt_it7495HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.58
X-RAY DIFFRACTIONt_other_torsion3.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1013SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8140SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.29 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3405 129 4.5 %
Rwork0.2727 2739 -
all0.2757 2868 -
obs--93.43 %
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)
17.0114-1.72990.03233.4753-0.07213.07370.01990.1174-0.2019-0.1017-0.07810.10440.1565-0.15440.0582-0.0123-0.11440.0092-0.14990.1328-0.1666-48.1517-32.54146.7779
22.6923-0.09340.0819-1.0042-0.45520.349-0.00420.01460.01790.0106-0.00860.0466-0.0131-0.0180.0128-0.0974-0.02940.010.1203-0.00490.1502-63.5974-31.129354.6494
30.9815-0.3499-0.43561.99190.3063.79710.0189-0.13330.00340.0520.0562-0.19450.0074-0.0545-0.0751-0.09150.03760.0207-0.08460.0359-0.0461-40.4516-11.910660.382
40.28661.3272-1.75024.7951-0.43962.5835-0.01510.0565-0.0221-0.0530.01710.06920.0513-0.0327-0.0020.083-0.08710.0337-0.06730.11810.0096-51.8724-24.20677.3311
54.81810.16592.14611.45760.21356.87980.0116-0.024-0.0353-0.01820.00220.10150.0736-0.0002-0.01380.02080.05790.0181-0.00540.115-0.252-50.3385-14.439572.0787
62.6876-1.3015-1.22230.41890.53932.79240.0070.0492-0.0457-0.0452-0.0306-0.02150.06550.01530.02360.12590.0219-0.123-0.00350.0127-0.0281-11.0706-55.591943.9174
75.34291.6395-0.08082.1657-0.63922.7952-0.00210.0009-0.05370.0194-0.0064-0.02660.08660.04740.00850.10940.0559-0.1444-0.25660.02-0.1414-16.911-55.029348.1829
8-0.19782.652.37463.1259-1.91731.8232-0.03350.0115-0.0437-0.00990.01410.07180.0097-0.06730.01940.1164-0.1456-0.1459-0.0683-0.03990.0413-31.4072-65.808955.3413
91.258-0.6573-0.3422.0406-0.01173.84970.179-0.11970.18530.0064-0.0217-0.25270.0083-0.0632-0.1572-0.066-0.029-0.0137-0.10770.0099-0.04-23.3842-34.647760.3646
103.6685-2.97371.56452.7975-2.39571.9246-0.00390.0522-0.0855-0.0354-0.03250.02660.10520.00780.03640.084-0.0359-0.1166-0.11550.0180.0437-24.3864-52.508177.5216
111.70042.17782.7293.7558-0.38976.40520.0145-0.011-0.1254-0.01010.03040.03340.01110.0206-0.04490.0679-0.1121-0.0752-0.05810.1033-0.2277-29.0519-43.375472.0822
125.87831.66060.30535.1724-1.21642.4684-0.06570.0669-0.2288-0.0544-0.0183-0.11770.16840.13030.0840.00420.1686-0.1415-0.2035-0.0202-0.032623.4298-53.64947.3436
13-0.6014-0.11521.47212.3856-2.48620.7941-0.03610.0175-0.04550.0393-0.01440.04370.0329-0.04450.05040.02090.0892-0.0032-0.01950.16550.108817.8388-68.724555.4446
142.4035-0.0165-0.77350.7901-0.53844.92460.0867-0.1880.33180.09350.05530.00180.07640.1473-0.142-0.1209-0.0361-0.0378-0.0776-0.0024-0.04124.3639-41.385560.4491
155.1037-1.57050.43070.2598-1.64162.80180.00330.0374-0.0528-0.0695-0.007-0.01630.04540.03630.0038-0.06210.048-0.09180.1373-0.0221-0.013914.8566-55.814377.3764
161.18880.0469-0.81463.39131.53015.6033-0.0061-0.0068-0.0880.0227-0.005-0.01760.00030.06880.0111-0.03760.02730.01250.12240.0075-0.26025.4716-51.892972.12
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 358:426
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 427:480
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 481:609
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 616:643
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 644:686
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 357:378
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 379:426
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 427:482
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 483:608
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 617:643
11X-RAY DIFFRACTION11CHAIN B AND RESSEQ 644:686
12X-RAY DIFFRACTION12CHAIN C AND RESSEQ 358:430
13X-RAY DIFFRACTION13CHAIN C AND RESSEQ 431:482
14X-RAY DIFFRACTION14CHAIN C AND RESSEQ 483:608
15X-RAY DIFFRACTION15CHAIN C AND RESSEQ 617:643
16X-RAY DIFFRACTION16CHAIN C AND RESSEQ 644:686

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