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- PDB-4pwu: Crystal structure of a modulator protein MzrA (KPN_03524) from Kl... -

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Basic information

Entry
Database: PDB / ID: 4pwu
TitleCrystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution
ComponentsModulator protein MzrA
KeywordsSIGNALING PROTEIN / ferredoxin-like fold / PF13721 family (SecD-TM1) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


protein kinase binding / plasma membrane
Similarity search - Function
Modulator protein MzrA / SecD export protein N-terminal TM domain / SecD export protein N-terminal TM region / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Modulator protein MzrA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Modulator protein MzrA
B: Modulator protein MzrA
C: Modulator protein MzrA
D: Modulator protein MzrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8407
Polymers42,5644
Non-polymers2763
Water30617
1
A: Modulator protein MzrA
B: Modulator protein MzrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3743
Polymers21,2822
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-11 kcal/mol
Surface area8840 Å2
MethodPISA
2
C: Modulator protein MzrA
D: Modulator protein MzrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4664
Polymers21,2822
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11 kcal/mol
Surface area8870 Å2
MethodPISA
3
A: Modulator protein MzrA
B: Modulator protein MzrA
hetero molecules

A: Modulator protein MzrA
B: Modulator protein MzrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7486
Polymers42,5644
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area3950 Å2
ΔGint-32 kcal/mol
Surface area16270 Å2
MethodPISA
4
C: Modulator protein MzrA
D: Modulator protein MzrA
hetero molecules

C: Modulator protein MzrA
D: Modulator protein MzrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9328
Polymers42,5644
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4380 Å2
ΔGint-36 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.770, 74.380, 74.200
Angle α, β, γ (deg.)90.000, 99.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-206-

HOH

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Components

#1: Protein
Modulator protein MzrA


Mass: 10640.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: mzrA, KPN78578_34950, KPN_03524 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6TED5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (32-128) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (32-128) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.98 Å3/Da / Density % sol: 37.76 %
Description: THE STRUCTURE WAS SOLVED BY THREE-WAVELENGTH MAD DATA COLLECTED AT 2.8A RESOLUTION, AND REFINED AGAINST A HIGHER RESOLUTION DATA (2.45A) COLLECTED FROM THE SAME CRYSTAL.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.83
Details: 1.40M sodium acetate, 0.1M sodium cacodylate pH 5.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL14-110.97934
SYNCHROTRONSSRL BL11-120.97959,0.91837,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2013
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979591
30.918371
40.978981
ReflectionResolution: 2.45→37.573 Å / Num. obs: 12229 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.56 % / Biso Wilson estimate: 66.057 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.45-2.517.671.4091.84685789499.9
2.51-2.581.2922661887099.2
2.58-2.660.9492.66645867100
2.66-2.740.5834.1629882499.5
2.74-2.830.4864.8617681399.8
2.83-2.930.3646.1572275699.3
2.93-3.040.2797.5578576899.6
3.04-3.160.2249.2525870099.3
3.16-3.30.13713.5533069999.6
3.3-3.460.09818513567799.1
3.46-3.650.0723.34767622100
3.65-3.870.06825460660899.7
3.87-4.140.05430.1419355999.8
4.14-4.470.048353946531100
4.47-4.90.04136.5359547998.8
4.9-5.480.04135.6330444399.6
5.48-6.330.04633.3283738299.7
6.33-7.750.03740.9251233899.7
7.75-10.960.0345186125499.6
10.96-37.570.03842.296714595.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.45→37.573 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9091 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. GLYCEROL(GOL) MODELED ARE PRESENT IN CRYO CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 556 4.55 %RANDOM
Rwork0.1989 ---
obs0.2013 12226 99.57 %-
Displacement parametersBiso max: 192.89 Å2 / Biso mean: 81.6489 Å2 / Biso min: 41.15 Å2
Baniso -1Baniso -2Baniso -3
1--8.9987 Å20 Å21.2767 Å2
2--15.2875 Å20 Å2
3----6.2888 Å2
Refine analyzeLuzzati coordinate error obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.45→37.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 18 17 2360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes347HARMONIC5
X-RAY DIFFRACTIONt_it2388HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion311SEMIHARMONIC5
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_contact2603SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2388HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3225HARMONIC30.84
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion2.82
LS refinement shellResolution: 2.45→2.68 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2615 131 4.49 %
Rwork0.2232 2786 -
all0.2249 2917 -
obs--99.57 %
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)
14.9605-1.339-0.60248.31551.46225.0045-0.2035-0.5510.5090.00660.10850.258-0.03850.07840.09490.15260.12590.0267-0.2467-0.1096-0.19924.5361-22.5064-31.0689
27.51232.73492.39766.23411.31229.11860.06480.4004-0.50760.5370.11860.08840.36280.2301-0.18340.15560.0074-0.0391-0.304-0.032-0.175424.6601-39.012-42.9628
37.85773.34081.63698.3155-2.40425.4567-0.32170.56940.0256-0.0290.2598-0.04390.1579-0.11010.06190.0305-0.14750.0937-0.1351-0.0398-0.208212.5523-18.5437-5.119
44.2997-0.76141.02948.3155-2.5978.75790.1945-0.3248-0.1397-0.54560.14620.0023-0.1228-0.4012-0.3407-0.01010.0616-0.035-0.1704-0.0267-0.163311.7077-36.00345.6656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|33 - 108}A33 - 108
2X-RAY DIFFRACTION2{B|34 - 110}B34 - 110
3X-RAY DIFFRACTION3{C|34 - 111}C34 - 111
4X-RAY DIFFRACTION4{D|34 - 109}D34 - 109

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