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- PDB-2qvp: CRYSTAL STRUCTURE OF A PUTATIVE METALLOPEPTIDASE (SAMA_0725) FROM... -

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Basic information

Entry
Database: PDB / ID: 2qvp
TitleCRYSTAL STRUCTURE OF A PUTATIVE METALLOPEPTIDASE (SAMA_0725) FROM SHEWANELLA AMAZONENSIS SB2B AT 2.00 A RESOLUTION
ComponentsUncharacterized protein
KeywordsHYDROLASE / PUTATIVE METALLOPEPTIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
: / Succinylglutamate desuccinylase/Aspartoacylase catalytic domain / AstE/AspA barrel-sandwich hybrid domain / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinylglutamate desuccinylase/Aspartoacylase catalytic domain-containing protein
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_926603.1) from Shewanella amazonensis SB2B at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS BUT THEY DO NOT FORM OLIGOMERS BASED ON CRYSTAL PACKING ANALYSIS. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER 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 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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,08425
Polymers91,0193
Non-polymers2,06622
Water9,476526
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6244
Polymers30,3401
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0048
Polymers30,3401
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,45713
Polymers30,3401
Non-polymers1,11712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 74.750, 96.120
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 6 / Auth seq-ID: 7 - 271 / Label seq-ID: 8 - 272

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS BUT THEY DO NOT FORM OLIGOMERS BASED ON CRYSTAL PACKING ANALYSIS. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 30339.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: YP_926603.1, Sama_0725 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S3H7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 1.6M (NH4)2SO4, 20.0% Glycerol, 0.1M Acetate pH 4.6, 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: 0.91837, 0.97944
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979441
ReflectionResolution: 2→29.63 Å / Num. obs: 57061 / % possible obs: 92.8 % / Redundancy: 3.36 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2-2.070.5181.8719189199.5
2.07-2.150.4342.319546199.8
2.15-2.250.3682.710720153.8
2.25-2.370.3033.318632191.7
2.37-2.520.2524.120909199.9
2.52-2.710.1985.220392199.9
2.71-2.990.1337.221634199.8
2.99-3.420.07811.120982199.9
3.42-4.30.0515.517921185.7
4.3-29.630.03519.421955199.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.307 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.159
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES A1-A6, A273-A274, B1-B5, B273-B274, AND C1-C5 ARE DISORDERED AND HAVE NOT BEEN MODELLED. 4. TEN SULFATE ANIONS AND TWELVE GLYCEROL MOLECULES HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. DIFFRACTION DATA IMAGES WERE PROCESSED BY MASKING OUT REFLECTIONS IN RESOLUTION RANGES 3.89A-3.87A, 3.70A-3.64A, 2.26A-2.24A AND 2.24A-2.21A CORRESPONDING TO ICE RINGS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2870 5 %RANDOM
Rwork0.161 ---
all0.164 ---
obs0.164 57042 93.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.6 Å2
2---0.03 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6159 0 122 526 6807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216564
X-RAY DIFFRACTIONr_bond_other_d0.0040.024419
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.978938
X-RAY DIFFRACTIONr_angle_other_deg1.394310773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3655848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95923.941307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.754151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2041540
X-RAY DIFFRACTIONr_chiral_restr0.090.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021362
X-RAY DIFFRACTIONr_nbd_refined0.1770.31261
X-RAY DIFFRACTIONr_nbd_other0.1540.34726
X-RAY DIFFRACTIONr_nbtor_refined0.170.53093
X-RAY DIFFRACTIONr_nbtor_other0.0880.53296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5722
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2240.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.341
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.398
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.541
X-RAY DIFFRACTIONr_mcbond_it2.1534461
X-RAY DIFFRACTIONr_mcbond_other0.54531660
X-RAY DIFFRACTIONr_mcangle_it2.90356515
X-RAY DIFFRACTIONr_scbond_it5.36582674
X-RAY DIFFRACTIONr_scangle_it7.131112397
Refine LS restraints NCS

Ens-ID: 1 / Number: 3208 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.455
2BLOOSE POSITIONAL0.535
3CLOOSE POSITIONAL0.465
1ALOOSE THERMAL3.2510
2BLOOSE THERMAL2.6710
3CLOOSE THERMAL2.7610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 219 -
Rwork0.218 4225 -
obs-4444 99.89 %
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)
11.2621-0.0433-0.64360.74050.142.79470.04120.00190.053-0.0094-0.0324-0.0006-0.2525-0.1804-0.00880.02340.04850.01340.009-0.013-0.031918.47518.77-4.178
21.16750.04110.05180.72880.10580.8249-0.0028-0.0025-0.05570.00840.0286-0.04220.05490.0638-0.0258-0.08660.01960.0084-0.06950.0043-0.0482-0.4945.081-32.775
31.06690.15770.0260.65320.09760.7650.00280.07740.0781-0.07430.00830.0162-0.0487-0.001-0.0112-0.08990.00470.015-0.09890.0059-0.055723.90344.47836.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 272
2X-RAY DIFFRACTION2B14 - 272
3X-RAY DIFFRACTION3C14 - 274

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