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- PDB-4h7l: Crystal structure of Plim_4148 protein from Planctomyces limnophilus -

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Basic information

Entry
Database: PDB / ID: 4h7l
TitleCrystal structure of Plim_4148 protein from Planctomyces limnophilus
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / cupin
Function / homologyRmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / COPPER (II) ION / Cupin 2 conserved barrel domain protein
Function and homology information
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.452 Å
AuthorsMichalska, K. / Bigelow, L. / Bruno, C.J.P. / Moser, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2144
Polymers35,0872
Non-polymers1272
Water19811
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-53 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.091, 67.091, 109.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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Components

#1: Protein uncharacterized protein


Mass: 17543.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_4148 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: D5SZ58
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M Bis-Tris/HCl, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 10974 / Num. obs: 10779 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.93
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.18 / Num. unique all: 549 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
BUCCANEERmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: dev_1096)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.452→29.051 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 810 7.52 %random
Rwork0.1766 ---
all0.1804 10775 --
obs0.1804 10775 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.452→29.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 2 11 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141862
X-RAY DIFFRACTIONf_angle_d0.8532549
X-RAY DIFFRACTIONf_dihedral_angle_d15.311653
X-RAY DIFFRACTIONf_chiral_restr0.049288
X-RAY DIFFRACTIONf_plane_restr0.003327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.452-2.60550.29031350.24311625X-RAY DIFFRACTION98
2.6055-2.80650.30141390.2481645X-RAY DIFFRACTION99
2.8065-3.08870.31281440.23211637X-RAY DIFFRACTION99
3.0887-3.53490.23611380.19341665X-RAY DIFFRACTION99
3.5349-4.45110.23831300.15361670X-RAY DIFFRACTION98
4.4511-29.05330.15731240.14921723X-RAY DIFFRACTION96
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)
15.0908-0.88493.44473.7953-0.5947.36350.2880.0191-0.5004-0.3730.17220.53540.8250.0112-0.43580.60150.0297-0.05940.3381-0.0490.60013.645148.739113.7635
23.0081-1.23251.16431.5037-0.40233.37360.25240.0517-0.4141-0.17230.09710.4610.4979-0.1101-0.34330.55420.0709-0.07190.36150.0140.6607-9.423157.70348.0946
32.3589-0.52651.02484.24380.41862.1845-0.219-0.16220.60820.04290.2834-0.0263-0.5281-0.0797-0.00620.74050.0825-0.09510.4307-0.02490.5993-2.326172.405214.6805
48.2499-0.28351.36941.4877-1.94533.71690.2646-0.75750.5270.45140.17390.3918-0.6582-0.0515-0.48770.72220.10430.05770.4446-0.02780.63231.816169.545518.5079
52.6777-0.49152.91730.91390.75115.93880.29770.05550.3144-0.2757-0.1361-0.0928-0.63790.5003-0.28150.6-0.05560.07180.3955-0.07230.560213.474266.237627.4457
63.52190.3496-3.81415.13840.83144.4117-0.2475-0.177-0.1026-0.6727-0.88860.00520.05381.52450.82360.51760.0402-0.10070.6170.1180.56479.662861.045914.9594
72.27590.64031.21332.85190.31255.25780.01350.02910.1889-0.1586-0.0272-0.2707-0.25460.54310.02270.40.03180.01230.31060.00480.522713.869161.810521.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 124 )
3X-RAY DIFFRACTION3chain 'B' and (resid 11 through 29 )
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 63 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 72 )
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 127 )

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