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- PDB-2owp: Crystal structure of a cystatin-like fold protein (bxe_b1374) fro... -

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Basic information

Entry
Database: PDB / ID: 2owp
TitleCrystal structure of a cystatin-like fold protein (bxe_b1374) from burkholderia xenovorans lb400 at 2.00 A resolution
ComponentsHypothetical protein Bxe_B1374
KeywordsUNKNOWN FUNCTION / Cystatin-like fold / duf3225 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAtzH-like / AtzH-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Oxalurate catabolism protein HpxZ
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein Bxe_B1374 (YP_553940.1) from Burkholderia xenovorans LB400 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / 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 ...database_2 / 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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). EBI PISA ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Bxe_B1374
B: Hypothetical protein Bxe_B1374
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,31318
Polymers29,2522
Non-polymers1,06116
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-17 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.518, 80.518, 116.256
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MSE / End label comp-ID: MSE / Refine code: 2 / Auth seq-ID: 4 - 127 / Label seq-ID: 5 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsEBI PISA ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein Bxe_B1374


Mass: 14625.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: YP_553940.1, Bxe_B1374, Bxeno_B1622 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13MU9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: NANODROP, 0.8M K2HPO4, 0.2M Li2SO4, 1.2M NaH2PO4, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 9, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2→29.894 Å / Num. obs: 29640 / % possible obs: 98.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.057.50.7611609821360.7698
2.05-2.117.60.6650.91589720910.66598.2
2.11-2.177.60.5821.31544320360.58298.4
2.17-2.247.50.4521.71512820040.45298.3
2.24-2.317.60.4071.71436218960.40798.6
2.31-2.397.50.3412.21416018770.34198.8
2.39-2.487.50.2942.61367018130.29498.7
2.48-2.587.50.2612.91314417410.26198.8
2.58-2.77.50.2093.61257716780.20999.1
2.7-2.837.50.1764.31189515900.17699.1
2.83-2.987.50.1395.31155415360.13999.2
2.98-3.167.40.116.51081014580.1199.5
3.16-3.387.40.0887.91022113800.08899.5
3.38-3.657.40.088.4943112820.0899.5
3.65-47.30.0729868311930.07299.8
4-4.477.20.06410.3780110880.06499.6
4.47-5.167.10.0659.768709690.06599.9
5.16-6.3270.0768.857898300.07699.9
6.32-8.946.80.0669.344966650.06699.6
8.94-29.916.10.0619.922933770.06196.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→29.894 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.868 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141
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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO, SO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1504 5.1 %RANDOM
Rwork0.192 ---
all0.194 ---
obs0.194 29613 98.51 %-
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: 35.937 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å21.2 Å20 Å2
2--2.41 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 2→29.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 66 297 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222136
X-RAY DIFFRACTIONr_bond_other_d0.0020.021457
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.942887
X-RAY DIFFRACTIONr_angle_other_deg0.8933515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63523.26598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9571518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022341
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02437
X-RAY DIFFRACTIONr_nbd_refined0.2010.2406
X-RAY DIFFRACTIONr_nbd_other0.2080.21517
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2993
X-RAY DIFFRACTIONr_nbtor_other0.0880.21147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.28
X-RAY DIFFRACTIONr_mcbond_it2.06631535
X-RAY DIFFRACTIONr_mcbond_other0.413515
X-RAY DIFFRACTIONr_mcangle_it2.6752096
X-RAY DIFFRACTIONr_scbond_it5.0938943
X-RAY DIFFRACTIONr_scangle_it6.64911790
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
730TIGHT POSITIONAL0.050.05
902MEDIUM POSITIONAL0.440.5
730TIGHT THERMAL0.260.5
902MEDIUM THERMAL0.952
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 110 -
Rwork0.231 2026 -
obs-2136 97.49 %
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)
11.3085-0.34920.17630.761-0.23282.3139-0.0898-0.032-0.07730.02690.03640.04480.1889-0.06520.0534-0.28120.0179-0.0005-0.3126-0.0326-0.21431.23340.34659.397
21.4949-0.12360.25510.869-0.12032.3501-0.05770.17420.1360.0354-0.0172-0.0703-0.21880.08460.0749-0.2996-0.0087-0.0304-0.2849-0.0001-0.20864.80750.72843.893
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 128 / Label seq-ID: 1 - 129

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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