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- PDB-4esn: Crystal structure of a DUF1312 family protein (RUMGNA_02503) from... -

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Basic information

Entry
Database: PDB / ID: 4esn
TitleCrystal structure of a DUF1312 family protein (RUMGNA_02503) from Ruminococcus gnavus ATCC 29149 at 2.20 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / PROTEIN OF PF07009 FAMILY / DUF1312 / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyN-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / Sandwich / Mainly Beta / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (RUMGNA_02503) from Ruminococcus gnavus ATCC 29149 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 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_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.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: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8395
Polymers23,3532
Non-polymers4853
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-86 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.854, 63.090, 67.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein


Mass: 11676.683 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_02503 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7B4L9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 33-117 OF THE TARGET SEQUENCE. ANALYSIS OF THE PURIFIED PROTEIN BY MASS SPECTROMETRY AND GEL ELECTROPHORESIS SHOWS THAT WHILE THE MAJORITY OF THE PROTEIN WAS CLEAVED, THERE WAS SOME UNCLEAVED PROTEIN PRESENT. SINCE ELECTRON DENSITY WAS OBSERVED FOR RESIDUES -2 AND -1 IN BOTH CHAINS, THE TAG SEQUENCE IS INCLUDED IN THE SEQRES RECORDS. THE CRYSTAL MAY CONTAIN A MIXTURE OF TAG-ON AND TAG-OFF PROTEIN.

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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: 1.82 Å3/Da / Density % sol: 32.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium nitrate 20.0% polyethylene glycol 3350, 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: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→28.58 Å / Num. all: 9044 / Num. obs: 9044 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rsym value: 0.081 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.267.30.6951.147726560.69599
2.26-2.327.30.5661.445326250.56699.7
2.32-2.397.30.5141.545256210.51499.4
2.39-2.467.30.375243135920.37599.2
2.46-2.547.20.3232.442525910.32399.4
2.54-2.637.20.253.140565600.2599.6
2.63-2.737.20.1834.139895510.18399.4
2.73-2.847.20.1524.838555370.15299.8
2.84-2.977.20.1335.436335050.13399.7
2.97-3.117.10.1175.835034930.11799.7
3.11-3.287.20.091734194750.09199.8
3.28-3.487.10.0867.331304410.08699.8
3.48-3.7270.0768.429734230.07699.8
3.72-4.0270.078.827923980.0799.7
4.02-4.470.05910.125433640.05999.9
4.4-4.926.90.0610.622863310.0699.8
4.92-5.686.80.0661020403020.06699.9
5.68-6.966.60.0798.816732530.079100
6.96-9.846.30.05610.613362120.05699.3
9.84-28.585.50.06110.26261140.06190.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.58 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9477 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. POLYETHYLENE GLYCOL (PE4) FROM THE CRYOPROTECTANT AND CL IONS FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ZN ION WAS MODELED IN THE PUTATIVE ACTIVE CENTER OF EACH PROTOME BASED ON ANOMALOUS DIFFERENCE MAPS AND EXCITATION SCANS. 5. 11 C-TERMINAL RESIDUES OF A AND B MOLECULES WERE DISORDERED. 6. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.207 431 4.78 %RANDOM
Rwork0.182 ---
obs0.1833 9018 99.24 %-
Displacement parametersBiso max: 144.05 Å2 / Biso mean: 64.2073 Å2 / Biso min: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.1933 Å20 Å20 Å2
2---8.3969 Å20 Å2
3---7.2036 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 26 53 1257
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d608SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes179HARMONIC5
X-RAY DIFFRACTIONt_it1244HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion169SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1432SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1244HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1685HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion3.21
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2388 120 4.82 %
Rwork0.1977 2370 -
all0.1997 2490 -
obs--99.24 %
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)
14.6744-0.0469-1.07772.164-0.63557.1634-0.36-0.1395-0.18590.11770.1252-0.02690.3389-0.04720.2348-0.06120.02290.0293-0.07940.045-0.044227.08548.01813.5104
23.6875-0.0623-0.74833.4809-2.460112.46460.21320.0745-0.0565-0.0359-0.4915-0.50210.02320.1070.2783-0.09810.0095-0.048-0.16060.0978-0.048338.03151.047318.1546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-3 - 106
2X-RAY DIFFRACTION2{ B|* }B-2 - 106

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