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- PDB-2huj: Crystal structure of a protein of uknown function (NP_471338.1) f... -

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Basic information

Entry
Database: PDB / ID: 2huj
TitleCrystal structure of a protein of uknown function (NP_471338.1) from Listeria innocua at 1.74 A resolution
ComponentsLin2004 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NP_471338.1 / hypothetical protein / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyYppE-like / YppE-like / YppE-like superfamily / Bacterial domain of unknown function (DUF1798) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Lin2004 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.
Authors: Kozbial, P. / Xu, Q. / Chiu, H.J. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Deller, M. / Duan, L. ...Authors: Kozbial, P. / Xu, Q. / Chiu, H.J. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Deller, M. / Duan, L. / Elias, Y. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Reyes, R. / Rife, C.L. / Spraggon, G. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Wolf, G. / Zubieta, C. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin2004 protein


Theoretical massNumber of molelcules
Total (without water)17,2201
Polymers17,2201
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.110, 100.110, 66.916
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

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Components

#1: Protein Lin2004 protein


Mass: 17219.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: NP_471338.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92AB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1358.66
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop4.630.0% Glycerol, 5.6% PEG-4000, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop4.50.2M Ca(OAc)2, 30.0% PEG-400, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.000001
SYNCHROTRONSSRL BL11-120.979291, 0.918370, 0.978981
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000011
20.9792911
30.918371
40.9789811
ReflectionResolution: 1.74→29.424 Å / Num. obs: 20444 / % possible obs: 98.7 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.797.10.8520.9979413760.85296.8
1.79-1.837.10.5991.31030214500.59998.1
1.83-1.897.10.4621.6990413980.46297.7
1.89-1.957.10.3712971313610.37198.5
1.95-2.0110.90.4131.71460313340.41398.3
2.01-2.0812.20.3152.21571212880.31599.3
2.08-2.16140.2283.21756512520.22899
2.16-2.25140.1883.81688812090.18899.2
2.25-2.3513.80.1474.81610711650.14799.6
2.35-2.46140.1116.31581211330.11199.6
2.46-2.5913.70.0977.21444710530.09799.9
2.59-2.7513.70.0848.21410310280.08499.9
2.75-2.9413.60.0729.2131739700.07299.9
2.94-3.1813.60.0639.7121218890.06399.8
3.18-3.4813.30.05311.4110008250.05399.4
3.48-3.8913.10.0491299417600.04999.1
3.89-4.4912.40.05211.983586740.05298.8
4.49-5.512.80.05510.773135710.05598.1
5.5-7.78130.0531158324500.05397.1
7.78-29.4510.10.04212.726012580.04291.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→29.424 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.666 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.(3) THERE ARE SOME SMALL BLOBS OF UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES A25, A46, A93 AND A96. THEY COULD BE DISORDERED SOLVENT MOLECULES FROM CRYSTALLIZATION SOLUTION. (4) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1072 5.2 %RANDOM
Rwork0.173 ---
obs0.175 20422 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.343 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.74→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 0 97 1141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221082
X-RAY DIFFRACTIONr_bond_other_d0.0020.02954
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9561460
X-RAY DIFFRACTIONr_angle_other_deg0.79732219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0545124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7562460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.064158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.2330.2225
X-RAY DIFFRACTIONr_nbd_other0.160.2837
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2543
X-RAY DIFFRACTIONr_nbtor_other0.0820.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1430.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.211
X-RAY DIFFRACTIONr_mcbond_it2.1113654
X-RAY DIFFRACTIONr_mcbond_other0.4943250
X-RAY DIFFRACTIONr_mcangle_it2.73851014
X-RAY DIFFRACTIONr_scbond_it4.8258501
X-RAY DIFFRACTIONr_scangle_it6.86911446
LS refinement shellResolution: 1.734→1.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 72 -
Rwork0.256 1152 -
obs-1224 84.76 %
Refinement TLS params.Method: refined / Origin x: 28.7236 Å / Origin y: 60.981 Å / Origin z: 11.3069 Å
111213212223313233
T-0.047 Å20.0102 Å20.0515 Å2--0.0781 Å2-0.0275 Å2---0.0564 Å2
L1.1918 °20.1539 °2-0.4184 °2-1.3595 °2-0.3091 °2--1.9449 °2
S0.0582 Å °-0.1863 Å °0.0855 Å °0.0646 Å °0.0371 Å °-0.0077 Å °-0.2189 Å °0.0546 Å °-0.0952 Å °
Refinement TLS groupSelection: ALL

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