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- PDB-4i1a: Crystal Structure of the Apo Form of RapI -

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Basic information

Entry
Database: PDB / ID: 4i1a
TitleCrystal Structure of the Apo Form of RapI
ComponentsResponse regulator aspartate phosphatase I
KeywordsHYDROLASE / Tetratricopeptide repeat / Phosphatase / Spo0F
Function / homology
Function and homology information


phosphoprotein phosphatase activity / Hydrolases; Acting on ester bonds
Similarity search - Function
: / response regulator aspartate phosphatase H, N terminal / : / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...: / response regulator aspartate phosphatase H, N terminal / : / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Response regulator aspartate phosphatase I
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.443 Å
AuthorsParashar, V. / Jeffrey, P.D. / Neiditch, M.B.
CitationJournal: Plos Biol. / Year: 2013
Title: Conformational change-induced repeat domain expansion regulates rap phosphatase quorum-sensing signal receptors.
Authors: Parashar, V. / Jeffrey, P.D. / Neiditch, M.B.
History
DepositionNov 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Response regulator aspartate phosphatase I
B: Response regulator aspartate phosphatase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3214
Polymers93,2502
Non-polymers712
Water46826
1
A: Response regulator aspartate phosphatase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6602
Polymers46,6251
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Response regulator aspartate phosphatase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6602
Polymers46,6251
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-28 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.897, 141.209, 50.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Response regulator aspartate phosphatase I


Mass: 46625.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU05010, rapI, yddL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96649, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 150 mM KCl, 5 mM DTT, 5 mM MgCl2, 17% [w/v] PEG 3350, 200 mM lithium nitrate, and 120 mM Tris-HCl (pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 35843 / % possible obs: 99.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.051 / Χ2: 1.048 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.44-2.487.30.6417581.0121100
2.48-2.537.30.52718001.0111100
2.53-2.587.30.40717490.9951100
2.58-2.637.30.33917981.0081100
2.63-2.697.30.30417701.0081100
2.69-2.757.30.243175311100
2.75-2.827.30.20818270.9761100
2.82-2.897.30.15417680.9811100
2.89-2.987.30.12417961.0041100
2.98-3.077.30.09917861.0111100
3.07-3.187.20.08317961.0481100
3.18-3.317.30.06917791.1051100
3.31-3.467.20.05718141.1321100
3.46-3.647.20.05618071.0461100
3.64-3.877.20.05318051.155199.9
3.87-4.177.10.04918381.133199.8
4.17-4.596.90.03818111.229199.2
4.59-5.256.70.02818191.078199.3
5.25-6.626.90.02618641.031199.9
6.62-506.10.02417050.99185

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.443→42.268 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1786 4.99 %
Rwork0.2212 --
obs0.2236 35789 98.99 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.115 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 170.8 Å2 / Biso mean: 76.4379 Å2 / Biso min: 36.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.6177 Å2-0 Å20 Å2
2---7.0298 Å2-0 Å2
3---7.6476 Å2
Refinement stepCycle: LAST / Resolution: 2.443→42.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 2 26 5365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075447
X-RAY DIFFRACTIONf_angle_d0.8887299
X-RAY DIFFRACTIONf_chiral_restr0.067767
X-RAY DIFFRACTIONf_plane_restr0.003920
X-RAY DIFFRACTIONf_dihedral_angle_d16.6822050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4432-2.50930.31421270.26832562268999
2.5093-2.58310.28691220.240725892711100
2.5831-2.66650.2281330.231626472780100
2.6665-2.76180.28571460.223325622708100
2.7618-2.87230.30851420.235125952737100
2.8723-3.0030.26441390.225426412780100
3.003-3.16130.26391520.216126072759100
3.1613-3.35930.27551360.210226152751100
3.3593-3.61850.25721550.205926252780100
3.6185-3.98240.25991320.198226372769100
3.9824-4.55810.22391380.188926722810100
4.5581-5.74050.28861270.217926982825100
5.7405-42.27420.30321370.26822553269090
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)
12.325-1.44831.16382.3955-2.72027.8664-0.0675-1.00930.04391.09580.31850.2891-0.88011.2635-0.28330.6202-0.07230.14720.8145-0.23880.669747.215620.647641.1801
27.80341.381-1.11243.5824-4.65766.1093-0.0329-0.21481.0811-0.0230.6384-0.7361-1.38040.5212-0.3520.701-0.33430.25450.5006-0.2760.716341.131323.05529.5358
35.0508-0.4308-1.01571.3836-0.19062.7578-0.20920.30090.1946-1.13230.5781-0.8141-1.02040.9877-0.30160.7735-0.35180.37360.6991-0.2270.522338.786718.076117.8608
44.60940.7894-0.83657.8591.83273.7649-0.06320.1828-0.1957-0.64140.4025-0.3971-0.35520.6621-0.32310.41330.01090.04480.4833-0.19270.390929.17351.660814.2634
55.7643-2.4772-2.97147.60951.90188.64520.1022-0.1797-1.07240.72660.17550.40041.08610.0511-0.24460.39270.0636-0.02780.33610.03130.542519.556-4.163727.411
64.90344.24616.59786.68224.5489.6177-0.03380.0704-0.1455-0.0145-0.05210.25330.0436-0.1680.11880.32240.03810.06010.4055-0.01750.461411.75857.375629.0273
73.73181.9179-0.64328.0505-0.264.3826-0.1504-0.06930.23860.6002-0.1443-0.3735-0.29350.06890.22710.3431-0.0544-0.09270.2677-0.00860.246934.485145.776147.1909
82.19770.24261.06312.231.54493.38060.2029-0.61740.35510.0471-0.39080.6637-0.5091-0.74510.08190.4267-0.00140.27220.525-0.0960.64794.671926.777443.2666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 101:138)A101 - 138
2X-RAY DIFFRACTION2chain 'A' and (resseq 139:175)A139 - 175
3X-RAY DIFFRACTION3chain 'A' and (resseq 176:219)A176 - 219
4X-RAY DIFFRACTION4chain 'A' and (resseq 220:295)A220 - 295
5X-RAY DIFFRACTION5chain 'A' and (resseq 296:333)A296 - 333
6X-RAY DIFFRACTION6chain 'A' and (resseq 334:374)A334 - 374
7X-RAY DIFFRACTION7chain 'B' and (resseq 14:176)B14 - 176
8X-RAY DIFFRACTION8chain 'B' and (resseq 177:377)B177 - 377

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