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- PDB-4mx8: Crystal Structure of TroA-like Periplasmic Binding Protein Peripl... -

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Basic information

Entry
Database: PDB / ID: 4mx8
TitleCrystal Structure of TroA-like Periplasmic Binding Protein Peripla_BP_2 from Xylanimonas cellulosilytica
ComponentsPeriplasmic binding protein
KeywordsSOLUTE-BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-fold
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
FatB domain / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic binding protein
Similarity search - Component
Biological speciesXylanimonas cellulosilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.911 Å
AuthorsKim, Y. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of TroA-like Periplasmic Binding Protein Peripla_BP_2 from Xylanimonas cellulosilytica
Authors: Kim, Y. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein
B: Periplasmic binding protein
C: Periplasmic binding protein
D: Periplasmic binding protein
E: Periplasmic binding protein
F: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)199,9636
Polymers199,9636
Non-polymers00
Water4,216234
1
A: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)33,3271
Polymers33,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.663, 116.547, 177.158
Angle α, β, γ (deg.)90.00, 112.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Periplasmic binding protein


Mass: 33327.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylanimonas cellulosilytica (bacteria) / Strain: DSM 15894 / Gene: Xcel_1393 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D1BRG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 4.82 Å3/Da / Density % sol: 74.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 81145 / Num. obs: 81145 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 54.12 Å2 / Rsym value: 0.058 / Net I/σ(I): 11.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3931 / Rsym value: 0.601 / % possible all: 96.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
BUCCANEERmodel building
PHENIX(phenix.refine: dev_1367)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.911→49.37 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4013 4.99 %random
Rwork0.159 ---
obs0.161 80493 96.62 %-
all-80493 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.4 Å2
Refinement stepCycle: LAST / Resolution: 2.911→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13497 0 0 234 13731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813823
X-RAY DIFFRACTIONf_angle_d1.13718933
X-RAY DIFFRACTIONf_dihedral_angle_d16.1244840
X-RAY DIFFRACTIONf_chiral_restr0.0752224
X-RAY DIFFRACTIONf_plane_restr0.0042520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9112-2.94540.3261910.31741830192168
2.9454-2.98130.34891140.28852474258890
2.9813-3.01910.36781430.28872495263893
3.0191-3.05880.32161430.2612609275295
3.0588-3.10070.28211070.24962556266396
3.1007-3.1450.30821230.23672715283897
3.145-3.19190.26911330.23792571270497
3.1919-3.24180.2971430.21922671281497
3.2418-3.29490.25851230.21672620274397
3.2949-3.35170.23741470.20592645279297
3.3517-3.41270.23341410.18832676281797
3.4127-3.47830.24521310.18992598272997
3.4783-3.54930.22851380.16852651278997
3.5493-3.62640.21621300.16412673280398
3.6264-3.71080.19731550.15622633278898
3.7108-3.80350.18961450.14052674281997
3.8035-3.90630.19221620.13452656281898
3.9063-4.02120.15131380.12882704284299
4.0212-4.15090.13491540.11642683283799
4.1509-4.29920.17451260.11652734286099
4.2992-4.47120.14871510.107427002851100
4.4712-4.67460.15071500.105327212871100
4.6746-4.92080.13071340.102827392873100
4.9208-5.22880.14531500.116727362886100
5.2288-5.6320.13811410.12627362877100
5.632-6.19780.20221560.14627372893100
6.1978-7.09240.1991510.155327392890100
7.0924-8.92710.17411630.142427612924100
8.9271-49.37740.18241300.17222743287397
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)
13.46930.6582-0.66593.7474-0.33172.41270.0093-0.33760.01520.33920.0048-0.2044-0.17170.1256-0.01210.2463-0.0074-0.06220.2236-0.0640.2709-17.270738.6912185.3635
21.05670.656-03.48760.42884.242-0.13650.0855-0.041-0.4541-0.0452-0.11140.5169-0.30140.14970.3466-0.03760.06480.207-0.07010.5115-11.648432.2199160.227
33.0876-0.5725-0.09664.05310.81552.7502-0.0258-0.3126-0.17390.40870.0706-0.00230.1660.0407-0.03910.23760.0044-0.00380.2150.07810.2773-32.879910.2562185.2278
42.0915-1.36770.54792.3522-0.3094.63080.11470.2773-0.1493-0.2365-0.29010.1505-0.5405-0.24270.13360.24740.0727-0.06830.2879-0.01510.4854-41.34588.66160.0255
53.46220.04370.41572.3099-0.8341.18540.21580.401-0.2614-0.4165-0.0604-0.0580.30170.1469-0.14480.74890.0468-0.01480.6321-0.11150.2807-26.11613.302296.6522
62.37920.7490.77763.14271.06396.19350.3913-0.111-0.11270.4851-0.4436-0.0072-0.2374-0.12340.04460.8271-0.1264-0.12650.439-0.01610.3961-19.197712.6773120.8402
74.08260.02560.87473.0348-0.39112.6612-0.0361-0.34930.19740.29320.07570.07480.0031-0.2127-0.03990.2169-0.00090.08740.2483-0.0380.2976-49.615137.9596185.3745
83.66920.7164-0.40721.2518-0.17753.9118-0.24280.3690.1582-0.12850.05290.0546-0.02640.63450.1540.1991-0.05540.01990.36060.08930.4937-46.850946.07160.1192
92.5681-0.0211-1.14692.6331-0.54960.85120.04470.45780.0496-0.1810.12680.2798-0.0805-0.306-0.17370.68510.0115-0.09330.75550.08250.2771-51.882131.355797.6645
102.3958-0.84820.782.8412-0.93135.8485-0.4241-0.13840.06010.7180.410.13350.08120.26760.01560.74960.28050.05870.61020.12820.4434-53.803323.4543122.8052
112.7815-0.96441.24656.36120.23970.80930.13070.28280.16990.12050.0139-0.2675-0.23080.475-0.17030.7381-0.04990.12380.6974-0.01430.2607-19.233441.88198.0621
123.09210.4455-0.17772.5491.47252.1172-0.02410.30640.1095-0.50330.2653-0.099-0.33490.034-0.2230.7353-0.06620.11260.61970.03960.2668-23.915945.233997.2441
133.53940.1197-1.06581.9671-0.06395.9275-0.0284-0.91940.16130.0230.0587-0.01770.142-0.1901-0.03830.4012-0.07820.05780.8634-0.1150.4107-27.912849.4828122.8977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 313 )
3X-RAY DIFFRACTION3chain 'B' and (resid 12 through 152 )
4X-RAY DIFFRACTION4chain 'B' and (resid 153 through 313 )
5X-RAY DIFFRACTION5chain 'C' and (resid 13 through 134 )
6X-RAY DIFFRACTION6chain 'C' and (resid 135 through 313 )
7X-RAY DIFFRACTION7chain 'D' and (resid 12 through 152 )
8X-RAY DIFFRACTION8chain 'D' and (resid 153 through 313 )
9X-RAY DIFFRACTION9chain 'E' and (resid 13 through 152 )
10X-RAY DIFFRACTION10chain 'E' and (resid 153 through 313 )
11X-RAY DIFFRACTION11chain 'F' and (resid 13 through 68 )
12X-RAY DIFFRACTION12chain 'F' and (resid 69 through 152 )
13X-RAY DIFFRACTION13chain 'F' and (resid 153 through 313 )

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