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- PDB-3u7z: Crystal structure of a putative metal binding protein RUMGNA_0085... -

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Basic information

Entry
Database: PDB / ID: 3u7z
TitleCrystal structure of a putative metal binding protein RUMGNA_00854 (ZP_02040092.1) from Ruminococcus gnavus ATCC 29149 at 1.30 A resolution
Componentsputative metal binding protein RUMGNA_00854
KeywordsMETAL BINDING PROTEIN / THE BINDING PROTEIN / TRANSPORT PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4430 / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function (DUF4430) / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Beta Complex / Mainly Beta / metal ion binding / DUF4430 domain-containing protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative metal binding protein RUMGNA_00854 (ZP_02040092.1) from Ruminococcus gnavus ATCC 29149 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_alt_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_auth_seq_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative metal binding protein RUMGNA_00854
B: putative metal binding protein RUMGNA_00854
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,12722
Polymers22,1492
Non-polymers97720
Water3,009167
1
A: putative metal binding protein RUMGNA_00854
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,50110
Polymers11,0751
Non-polymers4279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative metal binding protein RUMGNA_00854
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,62612
Polymers11,0751
Non-polymers55111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.685, 30.474, 47.156
Angle α, β, γ (deg.)73.130, 83.790, 89.300
Int Tables number1
Space group name H-MP1

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Components

#1: Protein putative metal binding protein RUMGNA_00854


Mass: 11074.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_00854 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7AZY1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 32-131) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 32-131) 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 34.0% polyethylene glycol 400, 0.20M calcium acetate, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 23, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→29.504 Å / Num. all: 36776 / Num. obs: 36776 / % possible obs: 95 % / Redundancy: 2.5 % / Rsym value: 0.067 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.330.5891.2675426540.58992.2
1.33-1.370.4961.4655525810.49692.4
1.37-1.410.4211.7646125400.42193.1
1.41-1.450.3392.1619324400.33993.4
1.45-1.50.2742.6611224100.27493.9
1.5-1.550.2083.5596623520.20894.5
1.55-1.610.1684.2565622200.16894.7
1.61-1.680.1425553421850.14295
1.68-1.750.116.3537421160.1195.7
1.75-1.840.0868508520120.08695.7
1.84-1.940.0729484819090.07296.2
1.94-2.060.0610.4462018240.0696.5
2.06-2.20.05610.9435817210.05697
2.2-2.370.05710.3408716130.05797.3
2.37-2.60.05511.3373914840.05597.6
2.6-2.910.05410.9340013480.05498.1
2.91-3.360.0511.3305112060.0598.4
3.36-4.110.0451224819940.04598
4.11-5.810.0451219147680.04597.1
5.81-29.5040.04712.29833990.04791.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BB6

2bb6


Resolution: 1.3→29.504 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.805 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. ETHYLENE GLYCOL, CALCIUM MODELED IS PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS. 2. THERE IS SOME UNEXPLAINED,UNUSUAL DENSITY BETWEEN THE CYS100/SG AND LYS128/NZ. 3. HYDROGENS HAVE BEEN ...Details: 1. ETHYLENE GLYCOL, CALCIUM MODELED IS PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS. 2. THERE IS SOME UNEXPLAINED,UNUSUAL DENSITY BETWEEN THE CYS100/SG AND LYS128/NZ. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 1824 5 %RANDOM
Rwork0.1379 ---
obs0.1404 36769 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.64 Å2 / Biso mean: 16.8017 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.13 Å2-0.09 Å2
2--0.06 Å2-0.14 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 44 167 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221655
X-RAY DIFFRACTIONr_bond_other_d0.0020.021060
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.952258
X-RAY DIFFRACTIONr_angle_other_deg1.05332634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66427.63493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33915275
X-RAY DIFFRACTIONr_chiral_restr0.1060.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
X-RAY DIFFRACTIONr_mcbond_it2.7313997
X-RAY DIFFRACTIONr_mcbond_other1.6733417
X-RAY DIFFRACTIONr_mcangle_it3.90251629
X-RAY DIFFRACTIONr_scbond_it4.8075658
X-RAY DIFFRACTIONr_scangle_it6.8778615
X-RAY DIFFRACTIONr_rigid_bond_restr2.17732715
X-RAY DIFFRACTIONr_sphericity_free9.4343186
X-RAY DIFFRACTIONr_sphericity_bonded4.22532681
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 124 -
Rwork0.231 2526 -
all-2650 -
obs--92.14 %

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