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- PDB-1m3d: Structure of Type IV Collagen NC1 Domains -

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Basic information

Entry
Database: PDB / ID: 1m3d
TitleStructure of Type IV Collagen NC1 Domains
Components(Type IV Collagen Noncollagenous Domain- ...) x 2
KeywordsSTRUCTURAL PROTEIN / Basement membrane / Type IV collagen / NC1 domain / Network assembly / 3D domain swapping / Br-MAD
Function / homology
Function and homology information


Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / Crosslinking of collagen fibrils / Laminin interactions / Non-integrin membrane-ECM interactions / Collagen degradation / extracellular matrix structural constituent conferring tensile strength ...Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / Crosslinking of collagen fibrils / Laminin interactions / Non-integrin membrane-ECM interactions / Collagen degradation / extracellular matrix structural constituent conferring tensile strength / collagen trimer / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / extracellular space / extracellular region
Similarity search - Function
Protein NDNF / Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) ...Protein NDNF / Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin fold / Beta Complex / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / : / Collagen alpha-1(IV) chain / Collagen alpha-2(IV) chain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSundaramoorthy, M. / Meiyappan, M. / Todd, P. / Hudson, B.G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of NC1 Domains. Structural Basis for Type IV Collagen Assembly in Basement Membranes
Authors: Sundaramoorthy, M. / Meiyappan, M. / Todd, P. / Hudson, B.G.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Remark 999SEQUENCE Authors informed that the alpha1 and alpha2 sequences are not available in standard ...SEQUENCE Authors informed that the alpha1 and alpha2 sequences are not available in standard reference sequence databases. However, sequences of overlapping fragments are available in NCBI's Expressed Sequence Tag (EST) databank from which complete sequences can be constructured. The accession numbers are: alpha1 - BE589226, BE846087, BE84675 alpha2 - BF039765, BM956598, AV613094

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type IV Collagen Noncollagenous Domain- Alpha1
B: Type IV Collagen Noncollagenous Domain- Alpha1
C: Type IV Collagen Noncollagenous Domain- Alpha2
D: Type IV Collagen Noncollagenous Domain- Alpha1
E: Type IV Collagen Noncollagenous Domain- Alpha1
F: Type IV Collagen Noncollagenous Domain- Alpha2
G: Type IV Collagen Noncollagenous Domain- Alpha1
H: Type IV Collagen Noncollagenous Domain- Alpha1
I: Type IV Collagen Noncollagenous Domain- Alpha2
J: Type IV Collagen Noncollagenous Domain- Alpha1
K: Type IV Collagen Noncollagenous Domain- Alpha1
L: Type IV Collagen Noncollagenous Domain- Alpha2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,84660
Polymers303,53312
Non-polymers4,31348
Water20,5011138
1
A: Type IV Collagen Noncollagenous Domain- Alpha1
B: Type IV Collagen Noncollagenous Domain- Alpha1
C: Type IV Collagen Noncollagenous Domain- Alpha2
D: Type IV Collagen Noncollagenous Domain- Alpha1
E: Type IV Collagen Noncollagenous Domain- Alpha1
F: Type IV Collagen Noncollagenous Domain- Alpha2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,92330
Polymers151,7676
Non-polymers2,15724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39450 Å2
ΔGint-212 kcal/mol
Surface area37770 Å2
MethodPISA
2
G: Type IV Collagen Noncollagenous Domain- Alpha1
H: Type IV Collagen Noncollagenous Domain- Alpha1
I: Type IV Collagen Noncollagenous Domain- Alpha2
J: Type IV Collagen Noncollagenous Domain- Alpha1
K: Type IV Collagen Noncollagenous Domain- Alpha1
L: Type IV Collagen Noncollagenous Domain- Alpha2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,92330
Polymers151,7676
Non-polymers2,15724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39300 Å2
ΔGint-211 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.069, 137.963, 127.131
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Type IV Collagen Noncollagenous Domain- ... , 2 types, 12 molecules ABDEGHJKCFIL

#1: Protein
Type IV Collagen Noncollagenous Domain- Alpha1


Mass: 25399.893 Da / Num. of mol.: 8 / Fragment: NC1 domain (Residues 1-229) / Source method: isolated from a natural source / Details: Bovine Eye Lens Capsule / Source: (natural) Bos taurus (cattle) / References: UniProt: Q7SIB2
#2: Protein
Type IV Collagen Noncollagenous Domain- Alpha2


Mass: 25083.541 Da / Num. of mol.: 4 / Fragment: NC1 domain (Residues 1-227) / Source method: isolated from a natural source / Details: Bovine Eye Lens Capsule / Source: (natural) Bos taurus (cattle) / References: UniProt: Q7SIB3

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Non-polymers , 4 types, 1186 molecules

#3: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Lu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20K, bicine buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %(w/v)PEG200001reservoir
30.1 MBicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8856, 0.9195, 0.9197, 0.9537
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2000 / Details: monochromator
RadiationMonochromator: Double crystal Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.91951
30.91971
40.95371
ReflectionResolution: 2→69.25 Å / Num. all: 184445 / Num. obs: 184445 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.72 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 30.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 13.1 / Num. unique all: 16498 / % possible all: 87.8
Reflection
*PLUS
Num. measured all: 686286
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→8 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 277228.26 / Data cutoff high rms absF: 277228.26 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 8789 5 %Random
Rwork0.169 ---
all0.174 179164 --
obs0.171 175237 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.5032 Å2 / ksol: 0.575522 e/Å3
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å2-0.21 Å2
2--2.13 Å20 Å2
3----1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20755 0 88 1138 21981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.293
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_dihedral_angle_d25.686
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.204 1380 5 %
Rwork0.159 25959 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion1.param
X-RAY DIFFRACTION4gol.param
Refinement
*PLUS
Num. reflection obs: 166448 / % reflection Rfree: 5 % / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0051
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.686
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Highest resolution: 2 Å

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