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- PDB-6pzj: Structure of the N-terminal domain (residues 43-304) of Methyl-ac... -

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Basic information

Entry
Database: PDB / ID: 6pzj
TitleStructure of the N-terminal domain (residues 43-304) of Methyl-accepting chemotaxis protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction
Similarity search - Function
Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of the N-terminal domain (residues 43-304) of Methyl-accepting chemotaxis protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8294
Polymers31,6701
Non-polymers1603
Water3,981221
1
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6598
Polymers63,3392
Non-polymers3196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4390 Å2
ΔGint-31 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.090, 72.090, 116.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 31669.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria)
Strain: Fiocruz L1-130 / Gene: mcpA, LIC_12921 / Plasmid: LpinA.18975.a.B2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q72NB4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: RigakuReagents JCSG+ screen A7: 20% (w/V) PEG 8000, 100mM CHES / NaOH pH 9.5: LpinA.18975.a.B2.PW38653 at 19.51mg/ml: cryo: 20% EG in 2 steps: tray 310977 a7: puck hqx5-3. For phasing: ...Details: RigakuReagents JCSG+ screen A7: 20% (w/V) PEG 8000, 100mM CHES / NaOH pH 9.5: LpinA.18975.a.B2.PW38653 at 19.51mg/ml: cryo: 20% EG in 2 steps: tray 310977 a7: puck hqx5-3. For phasing: Microlytic MCSG1 screen condition H3: 20% (w/V) PEG 3350, 200mM Lithium acetate: LpinA.18975.a.B2.PW38653 at 19.51mg/ml. A crystal from this condition was soaked for 15sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, and for another 15sec in a mix of 80% reservoir and 20% 2.5M NaI in EG, and flash frozen for in-house data collection: tray 310978 h3: puck hqx5-12

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDJul 18, 2019
RIGAKU SATURN 944+2CCDJul 18, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C(111)SINGLE WAVELENGTHMx-ray1
2Rigaku VariMaxSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.75→38.416 Å / Num. obs: 31892 / % possible obs: 100 % / Redundancy: 11.48 % / Biso Wilson estimate: 32.859 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.048 / Χ2: 1.056 / Net I/σ(I): 30.66 / Num. measured all: 366117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.87.9580.5993.1818455232023190.8750.641100
1.8-1.8410.090.4734.8922653224522450.9410.499100
1.84-1.911.8080.3796.8725990220122010.970.396100
1.9-1.9612.1990.289.5425972212921290.9830.293100
1.96-2.0212.1630.21412.5125201207220720.990.223100
2.02-2.0912.1780.17215.2624295199519950.9940.18100
2.09-2.1712.1440.12620.3323608194419440.9960.132100
2.17-2.2612.1360.10723.7722730187318730.9970.111100
2.26-2.3612.1630.08828.1321674178217820.9980.092100
2.36-2.4712.0810.07233.3920900173017300.9990.075100
2.47-2.6112.0670.06337.5619814164216420.9990.066100
2.61-2.7712.0060.05442.918909157515750.9990.056100
2.77-2.9611.9720.04649.9517443145714570.9990.048100
2.96-3.211.8230.03858.5916387138613860.9990.039100
3.2-3.511.6480.03265.46148741277127710.034100
3.5-3.9111.5710.02869.92134341161116110.029100
3.91-4.5211.3380.02674.69119161051105110.027100
4.52-5.5311.2430.02474.621008589789710.025100
5.53-7.8310.7650.02472.33770871671610.025100
7.83-38.4169.2480.02369.12406944944010.02498

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→38.416 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1984 6.23 %0
Rwork0.1652 ---
obs0.1677 31821 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.61 Å2 / Biso mean: 32.9902 Å2 / Biso min: 14.49 Å2
Refinement stepCycle: final / Resolution: 1.75→38.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 9 223 2364
Biso mean--43.73 44.15 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082243
X-RAY DIFFRACTIONf_angle_d0.9323052
X-RAY DIFFRACTIONf_dihedral_angle_d12.2241326
X-RAY DIFFRACTIONf_chiral_restr0.067315
X-RAY DIFFRACTIONf_plane_restr0.006398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.75-1.79380.28661440.21892097
1.7938-1.84230.22871310.19582079
1.8423-1.89650.24041350.18282118
1.8965-1.95770.22831490.1772066
1.9577-2.02770.21791300.17492099
2.0277-2.10890.20861370.17722114
2.1089-2.20480.21151290.16872117
2.2048-2.32110.2081220.1682137
2.3211-2.46650.20381470.16892102
2.4665-2.65690.21571560.17092115
2.6569-2.92410.21771440.1692148
2.9241-3.34710.20991560.16532129
3.3471-4.21610.17941480.14592199
4.2161-38.40.19541560.16082317
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)
17.1855-5.98610.81887.6249-0.82941.68660.08220.04150.1534-0.1047-0.08060.1518-0.154-0.1577-0.00620.1872-0.0389-0.02510.1814-0.0390.1768-6.029410.574631.3803
22.28270.48691.09642.5877-0.26073.6947-0.00270.0781-0.30530.02730.1323-0.31870.14730.4131-0.10840.15040.01130.01420.2171-0.05830.229616.8404-3.307628.7532
33.61420.460.87112.33821.96684.481-0.06610.3580.0388-0.02560.1502-0.511-0.18810.73620.010.1682-0.03030.03310.3147-0.03970.319622.44884.975828.9013
42.7926-0.32440.53883.82940.12162.0854-0.0049-0.08130.04890.0810.0111-0.40840.04720.2041-0.03020.1522-0.0128-0.01580.2093-0.02940.192413.36287.515137.8559
53.1061-2.64120.55644.6249-0.79751.74830.27110.24970.1506-0.5217-0.1486-0.0222-0.2236-0.0338-0.05020.2259-0.0079-0.00110.17020.00450.15181.171219.938828.2208
62.5057-1.334-0.17563.43150.23181.88080.0218-0.13190.30190.04950.02580.1235-0.3740.013-0.00520.2362-0.01-0.00830.1746-0.0340.1616-3.237624.348638.225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 72 )A37 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 114 )A73 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 151 )A115 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 198 )A152 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 238 )A199 - 238
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 300 )A239 - 300

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