HEADER HYDROLASE 05-MAR-03 1OP9 TITLE COMPLEX OF HUMAN LYSOZYME WITH CAMELID VHH HL6 ANTIBODY FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HL6 CAMEL VHH FRAGMENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LYSOZYME C; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; COMPND 9 EC: 3.2.1.17; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 3 ORGANISM_COMMON: ARABIAN CAMEL; SOURCE 4 ORGANISM_TAXID: 9838; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: LYZ OR LZM; SOURCE 12 EXPRESSION_SYSTEM: ASPERGILLUS NIGER; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 5061 KEYWDS ANTIGEN-ANTIBODY COMPLEX, IMMUNOGLOBULIN, AMYLOID FIBRIL FORMATION KEYWDS 2 INHIBITION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.DUMOULIN,A.M.LAST,A.DESMYTER,K.DECANNIERE,D.CANET,G.LARSSON, AUTHOR 2 A.SPENCER,D.B.ARCHER,J.SASSE,S.MUYLDERMANS,L.WYNS,C.REDFIELD, AUTHOR 3 A.MATAGNE,C.V.ROBINSON,C.M.DOBSON REVDAT 4 16-AUG-23 1OP9 1 REMARK REVDAT 3 04-APR-18 1OP9 1 REMARK REVDAT 2 24-FEB-09 1OP9 1 VERSN REVDAT 1 14-OCT-03 1OP9 0 JRNL AUTH M.DUMOULIN,A.M.LAST,A.DESMYTER,K.DECANNIERE,D.CANET, JRNL AUTH 2 G.LARSSON,A.SPENCER,D.B.ARCHER,J.SASSE,S.MUYLDERMANS,L.WYNS, JRNL AUTH 3 C.REDFIELD,A.MATAGNE,C.V.ROBINSON,C.M.DOBSON JRNL TITL A CAMELID ANTIBODY FRAGMENT INHIBITS THE FORMATION OF JRNL TITL 2 AMYLOID FIBRILS BY HUMAN LYSOZYME JRNL REF NATURE V. 424 783 2003 JRNL REFN ISSN 0028-0836 JRNL PMID 12917687 JRNL DOI 10.1038/NATURE01870 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19296 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1055 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1945 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20015 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: ANTIBODY: 1JTO LYSOZYME: 133L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % W/V PEG4000, 0.2M IMIDAZOLE REMARK 280 MALATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.11300 REMARK 290 SMTRY3 2 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 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, B 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 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 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 49 CD - NE - CZ ANGL. DEV. = 48.7 DEGREES REMARK 500 ARG B 10 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 10 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET B 17 CA - CB - CG ANGL. DEV. = -10.9 DEGREES REMARK 500 MET B 17 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG B 21 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG B 21 CA - CB - CG ANGL. DEV. = 18.7 DEGREES REMARK 500 ARG B 62 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 122 NE - CZ - NH2 ANGL. DEV. = -5.2 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 VAL A 45 -56.14 -123.07 REMARK 500 ALA A 89 165.16 178.79 REMARK 500 LYS B 69 19.30 -140.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 NO DBREF WAS GIVEN FOR PROTEIN MOLECULE A SINCE THIS REMARK 999 IMMUNOGLOBULIN HEAVY CHAIN HAS VARIABLE REGION REMARK 999 SEE GB ENTRY GI:7263678 DBREF 1OP9 B 1 130 UNP P61626 LYSC_HUMAN 19 148 DBREF 1OP9 A 1 121 PDB 1OP9 1OP9 1 121 SEQRES 1 A 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 A 121 ALA GLY GLY SER LEU ARG LEU SER CYS SER ALA SER GLY SEQRES 3 A 121 TYR THR TYR ILE SER GLY TRP PHE ARG GLN ALA PRO GLY SEQRES 4 A 121 LYS GLU ARG GLU GLY VAL ALA ALA ILE ARG SER SER ASP SEQRES 5 A 121 GLY THR THR TYR TYR ALA ASP SER VAL LYS GLY ARG PHE SEQRES 6 A 121 THR ILE SER GLN ASP ASN ALA LYS ASN THR VAL TYR LEU SEQRES 7 A 121 GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA MET TYR SEQRES 8 A 121 TYR CYS ALA ALA THR GLU VAL ALA GLY TRP PRO LEU ASP SEQRES 9 A 121 ILE GLY ILE TYR ASP TYR TRP GLY GLN GLY THR GLU VAL SEQRES 10 A 121 THR VAL SER SER SEQRES 1 B 130 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS SEQRES 2 B 130 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA SEQRES 3 B 130 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN SEQRES 4 B 130 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR SEQRES 5 B 130 ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS SEQRES 6 B 130 ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA CYS HIS SEQRES 7 B 130 LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP SEQRES 8 B 130 ALA VAL ALA CYS ALA LYS ARG VAL VAL ARG ASP PRO GLN SEQRES 9 B 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN SEQRES 10 B 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL FORMUL 3 HOH *207(H2 O) HELIX 1 1 LYS A 84 THR A 88 5 5 HELIX 2 2 ASP A 104 TYR A 108 5 5 HELIX 3 3 GLU B 4 LEU B 15 1 12 HELIX 4 4 GLY B 19 ILE B 23 5 5 HELIX 5 5 SER B 24 SER B 36 1 13 HELIX 6 6 SER B 80 GLN B 86 5 7 HELIX 7 7 ILE B 89 ASP B 102 1 14 HELIX 8 8 GLN B 104 ALA B 108 5 5 HELIX 9 9 TRP B 109 CYS B 116 1 8 HELIX 10 10 VAL B 121 VAL B 125 5 5 SHEET 1 A 4 LEU A 4 SER A 7 0 SHEET 2 A 4 LEU A 18 ALA A 24 -1 O SER A 21 N SER A 7 SHEET 3 A 4 THR A 75 MET A 80 -1 O LEU A 78 N LEU A 20 SHEET 4 A 4 PHE A 65 ASP A 70 -1 N THR A 66 O GLN A 79 SHEET 1 B 5 THR A 54 TYR A 57 0 SHEET 2 B 5 GLU A 43 ARG A 49 -1 N ALA A 47 O TYR A 56 SHEET 3 B 5 ILE A 30 GLN A 36 -1 N SER A 31 O ILE A 48 SHEET 4 B 5 ALA A 89 THR A 96 -1 O TYR A 92 N PHE A 34 SHEET 5 B 5 TYR A 110 TRP A 111 -1 O TYR A 110 N ALA A 95 SHEET 1 C 6 THR A 54 TYR A 57 0 SHEET 2 C 6 GLU A 43 ARG A 49 -1 N ALA A 47 O TYR A 56 SHEET 3 C 6 ILE A 30 GLN A 36 -1 N SER A 31 O ILE A 48 SHEET 4 C 6 ALA A 89 THR A 96 -1 O TYR A 92 N PHE A 34 SHEET 5 C 6 THR A 115 SER A 120 -1 O THR A 115 N TYR A 91 SHEET 6 C 6 SER A 11 GLN A 13 1 N VAL A 12 O THR A 118 SHEET 1 D 3 THR B 43 ASN B 46 0 SHEET 2 D 3 SER B 51 TYR B 54 -1 O SER B 51 N ASN B 46 SHEET 3 D 3 ILE B 59 ASN B 60 -1 O ILE B 59 N TYR B 54 SSBOND 1 CYS A 22 CYS A 93 1555 1555 2.05 SSBOND 2 CYS B 6 CYS B 128 1555 1555 2.01 SSBOND 3 CYS B 30 CYS B 116 1555 1555 2.05 SSBOND 4 CYS B 65 CYS B 81 1555 1555 2.03 SSBOND 5 CYS B 77 CYS B 95 1555 1555 2.02 CRYST1 39.611 48.226 66.605 90.00 98.98 90.00 P 1 21 1 2 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 0.025250 0.000000 0.003990 0.00000 SCALE2 0.000000 0.020740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015200 0.00000