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- PDB-4h0a: Crystal structure of a cysteine-rich secretory protein (SAV1118) ... -

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Basic information

Entry
Database: PDB / ID: 4h0a
TitleCrystal structure of a cysteine-rich secretory protein (SAV1118) from Staphylococcus aureus subsp. aureus Mu50 at 1.90 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CAP protein family / cysteine-rich secretory proteins / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
CAP-associated domain / CAP-associated N-terminal / Pathogenesis-related Protein p14a / CAP / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (SAV1118) from Staphylococcus aureus subsp. aureus Mu50 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7687
Polymers74,4582
Non-polymers3105
Water4,972276
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4154
Polymers37,2291
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3533
Polymers37,2291
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.386, 78.189, 77.161
Angle α, β, γ (deg.)90.000, 94.320, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 37228.766 Da / Num. of mol.: 2 / Fragment: UNP residues 24-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1118 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q99UY5, UniProt: A0A0H3JR67*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-345 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.00M LiCl, 10.00% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9464,0.9795,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94641
20.97951
30.97931
ReflectionResolution: 1.9→29.181 Å / Num. obs: 52080 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.616 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.6431.71900810028194.2
1.97-2.050.3952.51968810282198
2.05-2.140.3013.3183409600196.8
2.14-2.250.1934.8188999897197.7
2.25-2.390.1456.1190219977197.4
2.39-2.580.10582001110490198
2.58-2.840.07311.31913510045197
2.84-3.250.04216.9188099971196.7
3.25-4.080.02526.6178439552193.6
4.08-29.1810.01933.6189609843194

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.181 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9374 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 6. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 8. THERE IS SOME UNMODELED ELECTRON DENSITY IN THE REGION NEAR PHE-87, VAL-304 AND GLN-227 IN BOTH CHAINS. 9. THE N-TERMINAL REGIONS (A29-A34 AND B25-B37) HAVE POOR ELECTRON DENSITY AND MAY CONTAIN REGISTER ERRORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 2666 5.12 %RANDOM
Rwork0.1931 ---
obs0.1945 52055 98.74 %-
Displacement parametersBiso max: 190.77 Å2 / Biso mean: 59.4636 Å2 / Biso min: 23.51 Å2
Baniso -1Baniso -2Baniso -3
1--6.3759 Å20 Å21.6828 Å2
2---1.2112 Å20 Å2
3---7.5871 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 20 276 5082
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2763SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1421HARMONIC5
X-RAY DIFFRACTIONt_it9778HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion638SEMIHARMONIC5
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_contact10208SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9778HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg17662HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion2.89
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2464 193 5.2 %
Rwork0.2342 3519 -
all0.2348 3712 -
obs--98.74 %
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)
12.12430.4316-0.89773.28170.66743.3780.1093-0.28130.11240.8863-0.0302-0.24780.35250.3919-0.07910.11030.0221-0.0867-0.2735-0.0284-0.323339.830922.32044.6594
21.0056-0.14440.69032.18360.10533.50120.08680.11980.0012-0.3514-0.1281-0.2310.11960.33720.04130.00860.0680.0469-0.18760.0235-0.210942.600416.3417-29.2338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 345
2X-RAY DIFFRACTION2B25 - 345

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