10 20 30 40 50 60 70 80 1XKU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 29-SEP-04 1XKU
TITLE CRYSTAL STRUCTURE OF THE DIMERIC PROTEIN CORE OF DECORIN, THE TITLE 2 ARCHETYPAL SMALL LEUCINE-RICH REPEAT PROTEOGLYCAN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DECORIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BONE PROTEOGLYCAN II, PG-S2; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: DCN; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK 293A; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: ADENOVIRUS
KEYWDS PROTEOGLYCAN, LEUCINE-RICH REPEAT, STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.G.SCOTT,P.A.MCEWAN,C.M.DODD,E.M.BERGMANN,P.N.BISHOP,J.BELLA
REVDAT 4 13-JUL-11 1XKU 1 VERSN REVDAT 3 24-FEB-09 1XKU 1 VERSN REVDAT 2 09-NOV-04 1XKU 1 JRNL REVDAT 1 02-NOV-04 1XKU 0
JRNL AUTH P.G.SCOTT,P.A.MCEWAN,C.M.DODD,E.M.BERGMANN,P.N.BISHOP, JRNL AUTH 2 J.BELLA JRNL TITL CRYSTAL STRUCTURE OF THE DIMERIC PROTEIN CORE OF DECORIN, JRNL TITL 2 THE ARCHETYPAL SMALL LEUCINE-RICH REPEAT PROTEOGLYCAN JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 15633 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15501918 JRNL DOI 10.1073/PNAS.0402976101
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.G.SCOTT,J.G.GROSSMANN,C.M.DODD,J.K.SHEEHAN,P.N.BISHOP REMARK 1 TITL LIGHT AND X-RAY SCATTERING SHOW DECORIN TO BE A DIMER IN REMARK 1 TITL 2 SOLUTION REMARK 1 REF J.BIOL.CHEM. V. 278 18353 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 12601001 REMARK 1 DOI 10.1074/JBC.M211936200
REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 24591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1253 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2371 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.92000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.575 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2470 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3352 ; 1.719 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2 ; 0.539 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 5.519 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;43.917 ;25.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 442 ;15.199 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;14.684 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 393 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1797 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1016 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2 ; 0.287 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1624 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2 ; 0.239 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 150 ; 0.147 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.250 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.132 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1587 ; 1.049 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1 ; 0.032 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2481 ; 1.632 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 990 ; 2.973 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 871 ; 4.702 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 22 A 200 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9538 12.1333 36.2715 REMARK 3 T TENSOR REMARK 3 T11: -0.1527 T22: -0.0084 REMARK 3 T33: -0.0113 T12: -0.0007 REMARK 3 T13: 0.0069 T23: -0.0448 REMARK 3 L TENSOR REMARK 3 L11: 0.6519 L22: 1.1294 REMARK 3 L33: 4.3774 L12: 0.0091 REMARK 3 L13: -0.2295 L23: 0.0189 REMARK 3 S TENSOR REMARK 3 S11: -0.0643 S12: 0.0574 S13: 0.0165 REMARK 3 S21: 0.0220 S22: -0.0576 S23: 0.2674 REMARK 3 S31: 0.0796 S32: -0.7408 S33: 0.1219 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 201 A 326 REMARK 3 ORIGIN FOR THE GROUP (A): 2.0981 16.0869 68.3309 REMARK 3 T TENSOR REMARK 3 T11: 0.1729 T22: -0.0781 REMARK 3 T33: -0.0174 T12: -0.0325 REMARK 3 T13: -0.0327 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 1.2581 L22: 3.4785 REMARK 3 L33: 3.9797 L12: 0.2958 REMARK 3 L13: 0.6580 L23: -1.0147 REMARK 3 S TENSOR REMARK 3 S11: -0.0568 S12: -0.1930 S13: 0.0746 REMARK 3 S21: 0.7388 S22: -0.1487 S23: -0.2582 REMARK 3 S31: -0.4300 S32: 0.0983 S33: 0.2056 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1XKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030469.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24593 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 33.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 10.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIR/AS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, TRIS, OCTYL-BETA-D- REMARK 280 GLUCOPYRANOSIDE, SODIUM AZIDE, PH 7.75, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.80450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.80450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.89000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.07250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.89000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.07250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.80450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.89000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.07250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.80450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.89000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.07250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE TWO-FOLD AXIS -X, Y, -Z+1/2
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.80450
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 803 LIES ON A SPECIAL POSITION.
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 GLU A 10 REMARK 465 HIS A 11 REMARK 465 PHE A 12 REMARK 465 PRO A 13 REMARK 465 GLU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 GLU A 17 REMARK 465 ILE A 18 REMARK 465 GLU A 19 REMARK 465 PRO A 20 REMARK 465 MET A 21 REMARK 465 GLY A 327 REMARK 465 ASN A 328 REMARK 465 TYR A 329 REMARK 465 LYS A 330
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 309 CD GLU A 309 OE1 0.159 REMARK 500 GLU A 309 CD GLU A 309 OE2 0.223 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 71 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TRP A 308 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 28 -19.91 91.19 REMARK 500 ASN A 62 -160.38 -126.60 REMARK 500 ASN A 86 -154.86 -115.74 REMARK 500 ASN A 131 -155.34 -120.66 REMARK 500 LEU A 157 130.01 -39.58 REMARK 500 THR A 181 -169.17 -117.46 REMARK 500 ASN A 202 -150.15 -103.14 REMARK 500 ASN A 226 -161.45 -118.28 REMARK 500 THR A 239 69.83 -115.13 REMARK 500 ASN A 250 -157.65 -133.88 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 805 DISTANCE = 5.02 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 802
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XCD RELATED DB: PDB REMARK 900 DIMERIC BOVINE TISSUE-EXTRACTED DECORIN, CRYSTAL FORM 1 REMARK 900 RELATED ID: 1XEC RELATED DB: PDB REMARK 900 DIMERIC BOVINE TISSUE-EXTRACTED DECORIN, CRYSTAL FORM 2
DBREF 1XKU A 1 330 UNP P21793 PGS2_BOVIN 31 360
SEQADV 1XKU VAL A 253 UNP P21793 ALA 283 SEE REMARK 999 SEQADV 1XKU LEU A 259 UNP P21793 VAL 289 SEE REMARK 999
SEQRES 1 A 330 ASP GLU ALA SER GLY ILE GLY PRO GLU GLU HIS PHE PRO SEQRES 2 A 330 GLU VAL PRO GLU ILE GLU PRO MET GLY PRO VAL CYS PRO SEQRES 3 A 330 PHE ARG CYS GLN CYS HIS LEU ARG VAL VAL GLN CYS SER SEQRES 4 A 330 ASP LEU GLY LEU GLU LYS VAL PRO LYS ASP LEU PRO PRO SEQRES 5 A 330 ASP THR ALA LEU LEU ASP LEU GLN ASN ASN LYS ILE THR SEQRES 6 A 330 GLU ILE LYS ASP GLY ASP PHE LYS ASN LEU LYS ASN LEU SEQRES 7 A 330 HIS THR LEU ILE LEU ILE ASN ASN LYS ILE SER LYS ILE SEQRES 8 A 330 SER PRO GLY ALA PHE ALA PRO LEU VAL LYS LEU GLU ARG SEQRES 9 A 330 LEU TYR LEU SER LYS ASN GLN LEU LYS GLU LEU PRO GLU SEQRES 10 A 330 LYS MET PRO LYS THR LEU GLN GLU LEU ARG VAL HIS GLU SEQRES 11 A 330 ASN GLU ILE THR LYS VAL ARG LYS SER VAL PHE ASN GLY SEQRES 12 A 330 LEU ASN GLN MET ILE VAL VAL GLU LEU GLY THR ASN PRO SEQRES 13 A 330 LEU LYS SER SER GLY ILE GLU ASN GLY ALA PHE GLN GLY SEQRES 14 A 330 MET LYS LYS LEU SER TYR ILE ARG ILE ALA ASP THR ASN SEQRES 15 A 330 ILE THR THR ILE PRO GLN GLY LEU PRO PRO SER LEU THR SEQRES 16 A 330 GLU LEU HIS LEU ASP GLY ASN LYS ILE THR LYS VAL ASP SEQRES 17 A 330 ALA ALA SER LEU LYS GLY LEU ASN ASN LEU ALA LYS LEU SEQRES 18 A 330 GLY LEU SER PHE ASN SER ILE SER ALA VAL ASP ASN GLY SEQRES 19 A 330 SER LEU ALA ASN THR PRO HIS LEU ARG GLU LEU HIS LEU SEQRES 20 A 330 ASN ASN ASN LYS LEU VAL LYS VAL PRO GLY GLY LEU ALA SEQRES 21 A 330 ASP HIS LYS TYR ILE GLN VAL VAL TYR LEU HIS ASN ASN SEQRES 22 A 330 ASN ILE SER ALA ILE GLY SER ASN ASP PHE CYS PRO PRO SEQRES 23 A 330 GLY TYR ASN THR LYS LYS ALA SER TYR SER GLY VAL SER SEQRES 24 A 330 LEU PHE SER ASN PRO VAL GLN TYR TRP GLU ILE GLN PRO SEQRES 25 A 330 SER THR PHE ARG CYS VAL TYR VAL ARG ALA ALA VAL GLN SEQRES 26 A 330 LEU GLY ASN TYR LYS
MODRES 1XKU ASN A 182 ASN GLYCOSYLATION SITE MODRES 1XKU ASN A 233 ASN GLYCOSYLATION SITE MODRES 1XKU ASN A 274 ASN GLYCOSYLATION SITE
HET NAG A 800 14 HET NAG A 801 14 HET NAG A 802 14 HET TRS A 968 8
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
HETSYN TRS TRIS BUFFER
FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *164(H2 O)
HELIX 1 1 ARG A 137 ASN A 142 1 6 HELIX 2 2 LYS A 158 ILE A 162 5 5 HELIX 3 3 GLY A 165 MET A 170 5 6 HELIX 4 4 ALA A 209 LYS A 213 5 5 HELIX 5 5 SER A 235 THR A 239 5 5 HELIX 6 6 GLN A 306 ILE A 310 5 5 HELIX 7 7 GLN A 311 ARG A 316 5 6 HELIX 8 8 VAL A 320 ALA A 322 5 3
SHEET 1 A14 GLN A 30 HIS A 32 0 SHEET 2 A14 VAL A 35 GLN A 37 -1 O GLN A 37 N GLN A 30 SHEET 3 A14 LEU A 56 ASP A 58 1 O ASP A 58 N VAL A 36 SHEET 4 A14 THR A 80 ILE A 82 1 O ILE A 82 N LEU A 57 SHEET 5 A14 ARG A 104 TYR A 106 1 O TYR A 106 N LEU A 81 SHEET 6 A14 GLU A 125 ARG A 127 1 O GLU A 125 N LEU A 105 SHEET 7 A14 VAL A 149 GLU A 151 1 O GLU A 151 N LEU A 126 SHEET 8 A14 TYR A 175 ARG A 177 1 O ARG A 177 N VAL A 150 SHEET 9 A14 GLU A 196 HIS A 198 1 O HIS A 198 N ILE A 176 SHEET 10 A14 LYS A 220 GLY A 222 1 O GLY A 222 N LEU A 197 SHEET 11 A14 GLU A 244 HIS A 246 1 O HIS A 246 N LEU A 221 SHEET 12 A14 VAL A 267 TYR A 269 1 O VAL A 267 N LEU A 245 SHEET 13 A14 GLY A 297 SER A 299 1 O GLY A 297 N VAL A 268 SHEET 14 A14 VAL A 324 GLN A 325 1 O GLN A 325 N VAL A 298 SHEET 1 B 2 LYS A 206 VAL A 207 0 SHEET 2 B 2 ALA A 230 VAL A 231 1 O ALA A 230 N VAL A 207
SSBOND 1 CYS A 25 CYS A 31 1555 1555 2.06 SSBOND 2 CYS A 29 CYS A 38 1555 1555 2.09 SSBOND 3 CYS A 284 CYS A 317 1555 1555 2.09
LINK ND2 ASN A 182 C1 NAG A 800 1555 1555 1.46 LINK ND2 ASN A 233 C1 NAG A 801 1555 1555 1.45 LINK ND2 ASN A 274 C1 NAG A 802 1555 1555 1.45
SITE 1 AC1 8 ASN A 155 PRO A 156 LYS A 158 ASN A 182 SITE 2 AC1 8 TRP A 308 HOH A 932 HOH A 948 HOH A 949 SITE 1 AC2 1 ASN A 233 SITE 1 AC3 1 ASN A 274
CRYST1 55.780 124.145 129.609 90.00 90.00 90.00 C 2 2 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.017928 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008055 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007716 0.00000