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- PDB-4qan: Crystal structure of a cystatin-like protein (RUMGNA_02398) from ... -

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Basic information

Entry
Database: PDB / ID: 4qan
TitleCrystal structure of a cystatin-like protein (RUMGNA_02398) from Ruminococcus gnavus ATCC 29149 at 2.10 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / divergent member of NTF2-like superfamily / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterized protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (RUMGNA_02398) from Ruminococcus gnavus ATCC 29149 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 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_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_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)90,0383
Polymers90,0142
Non-polymers241
Water4,630257
1
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)45,0071
Polymers45,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0312
Polymers45,0071
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.394, 109.013, 137.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A55 - 153
2116B55 - 153
1216A158 - 208
2216B158 - 208
1316A228 - 360
2316B228 - 360
1416A365 - 413
2416B365 - 413
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein /


Mass: 45007.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_02398, ZP_02041626.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7B4B4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS 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 32-420 OF 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate, 20.0% polyethylene glycol 3350, The additive is 0.1 M Cesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.9798,0.97917
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97981
30.979171
ReflectionResolution: 2.1→29.671 Å / Num. obs: 45198 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.714 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.8291.521028760393.5
2.17-2.260.6611.924336887397.3
2.26-2.360.4432.521122808695.1
2.36-2.490.3783.225572891197.6
2.49-2.640.2934.123500821297.6
2.64-2.850.1986.124845884597.9
2.85-3.130.124922113819595.8
3.13-3.590.06816.524984866897.5
3.59-4.510.03727.922605823295.1
4.510.02737.623851832294.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.671 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 13.469 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. MODELING OF MAGNESIUM (MG) ION IS SUPPORTED BY COORDINATION AND ITS PRESENCE IN CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 2271 5 %RANDOM
Rwork0.1913 ---
obs0.1937 45054 98.05 %-
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 max: 192 Å2 / Biso mean: 50.8766 Å2 / Biso min: 19.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---2.56 Å2-0 Å2
3---4.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5993 0 1 257 6251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026149
X-RAY DIFFRACTIONr_bond_other_d0.0010.025823
X-RAY DIFFRACTIONr_angle_refined_deg1.2242.0048316
X-RAY DIFFRACTIONr_angle_other_deg0.698313519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16725.986284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.852151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4821522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021259
X-RAY DIFFRACTIONr_mcbond_it2.614.8623042
X-RAY DIFFRACTIONr_mcbond_other2.6084.8623041
X-RAY DIFFRACTIONr_mcangle_it3.8729.0963803
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5105 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.525
LOOSE THERMAL3.5210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 152 -
Rwork0.308 3064 -
all-3216 -
obs--96.55 %
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)
12.39180.36220.70741.79810.01911.7331-0.0375-0.1290.13490.2838-0.02270.0369-0.21160.16570.06020.1349-0.02120.0390.1373-0.0130.079656.9433.95547.048
21.3049-0.1882-0.32643.1812-0.63831.0787-0.0994-0.2228-0.02440.35590.0968-0.15450.1604-0.07270.00260.15990.001-0.02810.1886-0.03520.022824.078-2.52949.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 415
2X-RAY DIFFRACTION2B44 - 415

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