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- PDB-4kv7: The crystal structure of a possible leucine/isoleucine/valine-bin... -

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Basic information

Entry
Database: PDB / ID: 4kv7
TitleThe crystal structure of a possible leucine/isoleucine/valine-binding protein from Rhodopirellula baltica SH 1
ComponentsProbable leucine/isoleucine/valine-binding protein
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyLeucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Probable leucine/isoleucine/valine-binding protein
Function and homology information
Biological speciesRhodopirellula baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsTan, K. / Mack, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible leucine/isoleucine/valine-binding protein from Rhodopirellula baltica SH 1
Authors: Tan, K. / Mack, J. / Endres, M. / Joachimiak, A.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable leucine/isoleucine/valine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5002
Polymers41,4541
Non-polymers461
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.984, 44.483, 57.913
Angle α, β, γ (deg.)76.22, 88.65, 77.54
Int Tables number1
Space group name H-MP1
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein Probable leucine/isoleucine/valine-binding protein


Mass: 41453.574 Da / Num. of mol.: 1 / Mutation: G402S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopirellula baltica (bacteria) / Strain: SH 1 / Gene: livK, RB7306 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pGrow7-K / References: UniProt: Q7UNW4
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M DL-Malic Acid, 20%(w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.2→22.8 Å / Num. all: 105324 / Num. obs: 105324 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 27
Reflection shellResolution: 1.2→1.21 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3127 / % possible all: 83.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→22.752 Å / SU ML: 0.09 / σ(F): 1.97 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 5288 5.02 %random
Rwork0.1481 ---
obs0.1489 105323 93.72 %-
all-105323 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→22.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 3 572 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062914
X-RAY DIFFRACTIONf_angle_d1.1223974
X-RAY DIFFRACTIONf_dihedral_angle_d12.2781083
X-RAY DIFFRACTIONf_chiral_restr0.073458
X-RAY DIFFRACTIONf_plane_restr0.005521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2001-1.21380.19781590.20432879X-RAY DIFFRACTION81
1.2138-1.22810.18341530.19713227X-RAY DIFFRACTION89
1.2281-1.2430.2031620.18453201X-RAY DIFFRACTION91
1.243-1.25880.22591860.18383304X-RAY DIFFRACTION92
1.2588-1.27530.1951840.18073198X-RAY DIFFRACTION92
1.2753-1.29280.19881570.17863332X-RAY DIFFRACTION93
1.2928-1.31130.18361770.16663283X-RAY DIFFRACTION92
1.3113-1.33080.19421820.16133311X-RAY DIFFRACTION93
1.3308-1.35160.15611580.15553293X-RAY DIFFRACTION92
1.3516-1.37380.17351590.15343326X-RAY DIFFRACTION94
1.3738-1.39750.15641610.14843342X-RAY DIFFRACTION93
1.3975-1.42290.15712000.1453306X-RAY DIFFRACTION94
1.4229-1.45020.15791700.14663331X-RAY DIFFRACTION93
1.4502-1.47980.16531710.14073351X-RAY DIFFRACTION94
1.4798-1.5120.1461930.14173315X-RAY DIFFRACTION95
1.512-1.54720.14471770.13663354X-RAY DIFFRACTION94
1.5472-1.58590.16841760.12973396X-RAY DIFFRACTION94
1.5859-1.62870.15191650.13183412X-RAY DIFFRACTION95
1.6287-1.67660.15311920.13343345X-RAY DIFFRACTION95
1.6766-1.73070.14721720.13743436X-RAY DIFFRACTION96
1.7307-1.79260.15741830.13993403X-RAY DIFFRACTION96
1.7926-1.86430.16921960.14513367X-RAY DIFFRACTION96
1.8643-1.94910.16511970.14813430X-RAY DIFFRACTION96
1.9491-2.05180.1651890.14443414X-RAY DIFFRACTION97
2.0518-2.18030.1661830.13633449X-RAY DIFFRACTION96
2.1803-2.34840.14351750.13983479X-RAY DIFFRACTION97
2.3484-2.58450.17681980.15143418X-RAY DIFFRACTION97
2.5845-2.95780.1861740.15523478X-RAY DIFFRACTION97
2.9578-3.72380.15271740.14413467X-RAY DIFFRACTION97
3.7238-22.75620.14641650.15413188X-RAY DIFFRACTION90
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)
11.3934-0.71630.83841.2162-0.5341.38980.00040.37030.1868-0.25310.01410.1006-0.1622-0.0733-0.03170.1849-0.0032-0.03730.16210.04040.1295-9.250528.701926.3565
21.07070.3108-0.08691.9311-0.32641.462-0.0010.1310.1059-0.18580.04320.1239-0.1273-0.0375-0.05120.10110.0042-0.01970.09260.00530.1092-5.885726.300732.3795
31.447-0.18260.27931.5954-0.63632.19660.02590.2555-0.1269-0.26670.01750.06580.1582-0.0087-0.04320.1342-0.0073-0.00520.1115-0.02450.0898-0.435815.78728.9373
42.0866-0.4841.15071.1882-1.46232.79870.04360.0661-0.0675-0.0777-0.0344-0.05850.12140.1408-0.0350.06010.00550.01020.0553-0.0150.07612.416316.001543.3414
52.12450.02820.10990.8479-0.1131.0025-0.0291-0.138-0.24860.02850.0279-0.02530.06010.0711-0.02710.08960.00970.00510.0820.01790.11037.79025.149752.2519
61.56870.00110.14591.1883-0.59491.3256-0.027-0.451-0.13750.28080.09830.161-0.038-0.0924-0.03810.13280.01750.0250.18090.02530.09730.052312.293359.8393
70.8748-0.06510.07820.8547-0.11970.9078-0.00780.06540.1595-0.0623-0.0166-0.0206-0.06640.04490.02010.0937-0.01210.00360.06850.00460.10494.444131.637937.5591
82.2867-0.4151-0.29092.5441-0.80692.37240.00640.08080.1604-0.12880.0327-0.2423-0.08820.1626-0.04570.1174-0.01310.01790.1479-0.00390.132915.360725.561735.566
94.3233-0.6313-0.02163.763-0.56873.2794-0.0178-0.52910.2260.55150.0796-0.1576-0.25420.0951-0.08180.1839-0.013-0.01810.1495-0.0550.143310.41926.089758.3677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 297 )
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 372 )
8X-RAY DIFFRACTION8chain 'A' and (resid 373 through 393 )
9X-RAY DIFFRACTION9chain 'A' and (resid 394 through 413 )

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