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- PDB-1vmf: CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION... -

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Basic information

Entry
Database: PDB / ID: 1vmf
TitleCRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyYjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta / ACETATE ION / BH3498 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (10176122) from Bacillus halodurans at 1.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_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: hypothetical protein
B: hypothetical protein
C: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,25610
Polymers49,6913
Non-polymers5667
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-23 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.601, 58.951, 134.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein hypothetical protein


Mass: 16563.629 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K772

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Non-polymers , 5 types, 424 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3146.64
22.243.54TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2 A MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE INITIAL MODEL WAS THEN EXTENDED AND REBUILT WITH ARP/WARP USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 1.46 A. REFINEMENT WAS AGAINST THE 1.46 A DATA.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop7.58.0% Ethylene Glycol, 10.0% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop7.50.2M NaCl, 30.0% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.110.980075
SYNCHROTRONSSRL BL11-120.97957,0.979694,1.019859
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 11, 2004flat mirror
ADSC2CCDAug 27, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorMADMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9800751
20.979571
30.9796941
41.0198591
ReflectionResolution: 1.46→29.48 Å / Num. obs: 78750 / % possible obs: 97.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10604 / % possible all: 92

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
SHELXmodel building
SHARPphasing
REFMAC(5.2.0005)refinement
XDSdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.46→29.48 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.137 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17483 3955 5 %RANDOM
Rwork0.14832 ---
obs0.14964 74793 97.69 %-
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: 19.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.46→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 36 417 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213375
X-RAY DIFFRACTIONr_bond_other_d0.0020.023010
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9154585
X-RAY DIFFRACTIONr_angle_other_deg0.82636987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92223.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27515572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9021520
X-RAY DIFFRACTIONr_chiral_restr0.080.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
X-RAY DIFFRACTIONr_nbd_refined0.2170.2573
X-RAY DIFFRACTIONr_nbd_other0.1910.23099
X-RAY DIFFRACTIONr_nbtor_other0.0820.21982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.224
X-RAY DIFFRACTIONr_mcbond_it1.60832033
X-RAY DIFFRACTIONr_mcbond_other0.4353838
X-RAY DIFFRACTIONr_mcangle_it2.69253332
X-RAY DIFFRACTIONr_scbond_it3.9581390
X-RAY DIFFRACTIONr_scangle_it6.223111253
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21614
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.26
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 268 5.33 %
Rwork0.261 4762 -
obs--85.81 %
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)
10.5315-0.09170.17090.61890.01410.985-0.02030.09040.0211-0.1219-0.0211-0.0059-0.09670.03790.0413-0.0479-0.01-0.0015-0.02350.00690.012749.26317.1626.109
20.541-0.0620.30370.68220.27671.23970.0358-0.0825-0.06420.1078-0.01450.08680.1509-0.1569-0.0213-0.0476-0.0223-0.0058-0.02230.01320.029841.678.63622.556
30.62130.0640.44680.70850.2781.10670.03920.0506-0.03210.06140.0097-0.13610.05160.2062-0.0489-0.05330.0028-0.019-0.0152-0.00010.033561.1312.76921.658
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-2 - 13310 - 145
22BB-2 - 13310 - 145
33CC-1 - 13311 - 145

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