HEADER ANTIBODY, HYDROLASE 21-AUG-01 1JTP TITLE DEGENERATE INTERFACES IN ANTIGEN-ANTIBODY COMPLEXES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-DOMAIN ANTIBODY; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VH DOMAIN FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LYSOZYME C; COMPND 8 CHAIN: L, M; COMPND 9 FRAGMENT: ENZYME; COMPND 10 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; COMPND 11 EC: 3.2.1.17 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHEN1; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 11 ORGANISM_COMMON: TURKEY; SOURCE 12 ORGANISM_TAXID: 9103; SOURCE 13 OTHER_DETAILS: PURCHASED FROM SIGMA KEYWDS IMMUNOGLOBULIN, HEAVY CHAIN ANTIBODY, VHH, INTERFACE, ANTIBODY, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.DECANNIERE,T.R.TRANSUE,A.DESMYTER,D.MAES,S.MUYLDERMANS,L.WYNS REVDAT 4 16-AUG-23 1JTP 1 REMARK LINK REVDAT 3 04-OCT-17 1JTP 1 REMARK REVDAT 2 24-FEB-09 1JTP 1 VERSN REVDAT 1 05-DEC-01 1JTP 0 JRNL AUTH K.DECANNIERE,T.R.TRANSUE,A.DESMYTER,D.MAES,S.MUYLDERMANS, JRNL AUTH 2 L.WYNS JRNL TITL DEGENERATE INTERFACES IN ANTIGEN-ANTIBODY COMPLEXES. JRNL REF J.MOL.BIOL. V. 313 473 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11676532 JRNL DOI 10.1006/JMBI.2001.5075 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DESMYTER,T.R.TRANSUE,M.A.GHAHROUDI,M.H.THI,F.POORTMANS, REMARK 1 AUTH 2 R.HAMERS,S.MUYLDERMANS,L.WYNS REMARK 1 TITL CRYSTAL STRUCTURE OF A CAMEL SINGLE-DOMAIN VH ANTIBODY REMARK 1 TITL 2 FRAGMENT IN COMPLEX WITH LYSOZYME REMARK 1 REF NAT.STRUCT.BIOL. V. 3 803 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENG & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 10.2 REMARK 3 NUMBER OF REFLECTIONS : 40619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE-R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4149 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.08700 REMARK 3 B22 (A**2) : -0.16200 REMARK 3 B33 (A**2) : 4.25000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: OVERALL ANISOTROPIC B-FACTOR AND BULK REMARK 3 SOLVENT CORRECTION USED REMARK 4 REMARK 4 1JTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98089 REMARK 200 MONOCHROMATOR : 0.98089 ANGSTROM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40619 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : 0.41700 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB CODE: 1MEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M NA FORMATE, 100MM NA CITRATE, PH REMARK 280 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 33.56150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.61550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.68750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.61550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.56150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.68750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, M 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 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 TYR A 136 REMARK 465 PRO A 137 REMARK 465 TYR A 138 REMARK 465 ASP A 139 REMARK 465 VAL A 140 REMARK 465 PRO A 141 REMARK 465 ASP A 142 REMARK 465 TYR A 143 REMARK 465 GLY A 144 REMARK 465 SER A 145 REMARK 465 GLY A 146 REMARK 465 ARG A 147 REMARK 465 ALA A 148 REMARK 465 ARG B 134 REMARK 465 ARG B 135 REMARK 465 TYR B 136 REMARK 465 PRO B 137 REMARK 465 TYR B 138 REMARK 465 ASP B 139 REMARK 465 VAL B 140 REMARK 465 PRO B 141 REMARK 465 ASP B 142 REMARK 465 TYR B 143 REMARK 465 GLY B 144 REMARK 465 SER B 145 REMARK 465 GLY B 146 REMARK 465 ARG B 147 REMARK 465 ALA B 148 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 135 CB CG CD NE CZ NH1 NH2 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 PRO L 70 C - N - CA ANGL. DEV. = 13.4 DEGREES REMARK 500 PRO L 70 C - N - CD ANGL. DEV. = -17.3 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 ASN A 74 -60.84 65.62 REMARK 500 ALA A 92 173.14 175.56 REMARK 500 THR A 115 51.47 -113.33 REMARK 500 VAL B 2 107.09 85.14 REMARK 500 ALA B 92 171.13 176.19 REMARK 500 THR B 115 42.30 -102.88 REMARK 500 PRO L 70 -76.26 -8.44 REMARK 500 ASN L 74 63.77 -151.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 99 OD1 REMARK 620 2 GLY A 119 O 80.8 REMARK 620 3 ASP A 121 OD2 92.5 80.6 REMARK 620 4 HOH A 510 O 90.6 102.6 175.8 REMARK 620 5 HOH A 537 O 172.4 101.7 95.0 81.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 99 OD1 REMARK 620 2 GLY B 119 O 81.1 REMARK 620 3 ASP B 121 OD2 95.0 85.4 REMARK 620 4 HOH B 511 O 92.6 102.8 169.6 REMARK 620 5 HOH M 559 O 173.0 95.0 90.5 82.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA L 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 35 OE1 REMARK 620 2 FMT L 406 O1 78.5 REMARK 620 3 HOH L 526 O 125.7 154.1 REMARK 620 4 HOH L 551 O 125.5 59.0 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA L 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER L 60 O REMARK 620 2 CYS L 64 O 82.7 REMARK 620 3 SER L 72 OG 96.1 162.3 REMARK 620 4 LYS L 73 O 112.1 94.5 102.2 REMARK 620 5 HOH L 515 O 84.4 81.1 81.2 162.4 REMARK 620 6 HOH L 568 O 161.2 91.8 83.6 86.2 77.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA M 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER M 60 O REMARK 620 2 CYS M 64 O 79.8 REMARK 620 3 SER M 72 OG 90.0 160.0 REMARK 620 4 LYS M 73 O 114.5 95.9 104.0 REMARK 620 5 HOH M 520 O 72.7 83.6 76.9 172.6 REMARK 620 6 HOH M 533 O 152.8 101.0 80.3 92.6 80.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA L 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA M 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA L 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT M 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT M 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT M 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT L 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MEL RELATED DB: PDB REMARK 900 THIS STRUCTURE IS ISOMOROPHOUS AND CONTAINS THE SAME ANTIBODY. THE REMARK 900 LYSOZYME MOLECULES ARE FROM DIFFERENT SPECIES REMARK 900 RELATED ID: 1JTO RELATED DB: PDB REMARK 900 1JTO IS A RE-REFINED VERSION OF 1MEL WHICH IS ISOMOROPHOUS AND REMARK 900 CONTAINS THE SAME ANTIBODY. THE LYSOZYME MOLECULES ARE FROM REMARK 900 DIFFERENT SPECIES REMARK 999 REMARK 999 SEQUENCE REMARK 999 ARG IS PART OF THE REMARK 999 HEMAGLUTAMINE-TAG, WHILE THE REMARK 999 ENTRY IN THE GB DATABASE REMARK 999 REPRESENTS THE SAME MOLECULE REMARK 999 WITH A HIS-TAG. DBREF 1JTP A 1 148 GB 2392447 2392447 1 148 DBREF 1JTP B 1 148 GB 2392447 2392447 1 148 DBREF 1JTP L 1 129 UNP P00703 LYSC_MELGA 19 147 DBREF 1JTP M 1 129 UNP P00703 LYSC_MELGA 19 147 SEQADV 1JTP ARG A 134 UNP 2392447 GLY 134 SEE REMARK 999 SEQADV 1JTP ARG B 134 UNP 2392447 GLY 134 SEE REMARK 999 SEQRES 1 A 148 ASP VAL GLN LEU GLN ALA SER GLY GLY GLY SER VAL GLN SEQRES 2 A 148 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 148 TYR THR ILE GLY PRO TYR CYS MET GLY TRP PHE ARG GLN SEQRES 4 A 148 ALA PRO GLY LYS GLU ARG GLU GLY VAL ALA ALA ILE ASN SEQRES 5 A 148 MET GLY GLY GLY ILE THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 148 GLY ARG PHE THR ILE SER GLN ASP ASN ALA LYS ASN THR SEQRES 7 A 148 VAL TYR LEU LEU MET ASN SER LEU GLU PRO GLU ASP THR SEQRES 8 A 148 ALA ILE TYR TYR CYS ALA ALA ASP SER THR ILE TYR ALA SEQRES 9 A 148 SER TYR TYR GLU CYS GLY HIS GLY LEU SER THR GLY GLY SEQRES 10 A 148 TYR GLY TYR ASP SER TRP GLY GLN GLY THR GLN VAL THR SEQRES 11 A 148 VAL SER SER ARG ARG TYR PRO TYR ASP VAL PRO ASP TYR SEQRES 12 A 148 GLY SER GLY ARG ALA SEQRES 1 B 148 ASP VAL GLN LEU GLN ALA SER GLY GLY GLY SER VAL GLN SEQRES 2 B 148 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 148 TYR THR ILE GLY PRO TYR CYS MET GLY TRP PHE ARG GLN SEQRES 4 B 148 ALA PRO GLY LYS GLU ARG GLU GLY VAL ALA ALA ILE ASN SEQRES 5 B 148 MET GLY GLY GLY ILE THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 148 GLY ARG PHE THR ILE SER GLN ASP ASN ALA LYS ASN THR SEQRES 7 B 148 VAL TYR LEU LEU MET ASN SER LEU GLU PRO GLU ASP THR SEQRES 8 B 148 ALA ILE TYR TYR CYS ALA ALA ASP SER THR ILE TYR ALA SEQRES 9 B 148 SER TYR TYR GLU CYS GLY HIS GLY LEU SER THR GLY GLY SEQRES 10 B 148 TYR GLY TYR ASP SER TRP GLY GLN GLY THR GLN VAL THR SEQRES 11 B 148 VAL SER SER ARG ARG TYR PRO TYR ASP VAL PRO ASP TYR SEQRES 12 B 148 GLY SER GLY ARG ALA SEQRES 1 L 129 LYS VAL TYR GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 L 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 L 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 L 129 THR HIS ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 L 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 L 129 ASP GLY ARG THR PRO GLY SER LYS ASN LEU CYS ASN ILE SEQRES 7 L 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 L 129 VAL ASN CYS ALA LYS LYS ILE ALA SER GLY GLY ASN GLY SEQRES 9 L 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 L 129 THR ASP VAL HIS ALA TRP ILE ARG GLY CYS ARG LEU SEQRES 1 M 129 LYS VAL TYR GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 M 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 M 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 M 129 THR HIS ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 M 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 M 129 ASP GLY ARG THR PRO GLY SER LYS ASN LEU CYS ASN ILE SEQRES 7 M 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 M 129 VAL ASN CYS ALA LYS LYS ILE ALA SER GLY GLY ASN GLY SEQRES 9 M 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 M 129 THR ASP VAL HIS ALA TRP ILE ARG GLY CYS ARG LEU HET NA A 501 1 HET FMT A 401 3 HET NA B 502 1 HET FMT B 402 3 HET NA L 503 1 HET NA L 505 1 HET FMT L 406 3 HET NA M 504 1 HET FMT M 403 3 HET FMT M 404 3 HET FMT M 405 3 HETNAM NA SODIUM ION HETNAM FMT FORMIC ACID FORMUL 5 NA 5(NA 1+) FORMUL 6 FMT 6(C H2 O2) FORMUL 16 HOH *298(H2 O) HELIX 1 1 ASP A 62 LYS A 65 5 4 HELIX 2 2 GLU A 87 THR A 91 5 5 HELIX 3 3 CYS A 109 THR A 115 1 7 HELIX 4 4 GLU B 87 THR B 91 5 5 HELIX 5 5 CYS B 109 THR B 115 1 7 HELIX 6 6 GLY L 4 LEU L 15 1 12 HELIX 7 7 ASN L 19 TYR L 23 5 5 HELIX 8 8 SER L 24 ASN L 37 1 14 HELIX 9 9 PRO L 79 SER L 85 5 7 HELIX 10 10 ILE L 88 SER L 100 1 13 HELIX 11 11 ASN L 103 ALA L 107 5 5 HELIX 12 12 TRP L 108 CYS L 115 1 8 HELIX 13 13 ASP L 119 ARG L 125 5 7 HELIX 14 14 GLY M 4 LEU M 15 1 12 HELIX 15 15 ASN M 19 TYR M 23 5 5 HELIX 16 16 SER M 24 ASN M 37 1 14 HELIX 17 17 PRO M 79 SER M 85 5 7 HELIX 18 18 ILE M 88 ALA M 99 1 12 HELIX 19 19 ASN M 103 ALA M 107 5 5 HELIX 20 20 TRP M 108 CYS M 115 1 8 HELIX 21 21 ASP M 119 ILE M 124 5 6 SHEET 1 A 4 GLN A 3 SER A 7 0 SHEET 2 A 4 LEU A 18 SER A 25 -1 O ALA A 23 N GLN A 5 SHEET 3 A 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 A 4 PHE A 68 GLN A 72 -1 N THR A 69 O LEU A 82 SHEET 1 B 5 THR A 58 TYR A 60 0 SHEET 2 B 5 GLU A 46 ASN A 52 -1 N ALA A 50 O TYR A 59 SHEET 3 B 5 CYS A 33 GLN A 39 -1 N ARG A 38 O GLU A 46 SHEET 4 B 5 ALA A 92 ASP A 99 -1 O TYR A 95 N PHE A 37 SHEET 5 B 5 SER A 122 TRP A 123 -1 O SER A 122 N ALA A 98 SHEET 1 C 6 THR A 58 TYR A 60 0 SHEET 2 C 6 GLU A 46 ASN A 52 -1 N ALA A 50 O TYR A 59 SHEET 3 C 6 CYS A 33 GLN A 39 -1 N ARG A 38 O GLU A 46 SHEET 4 C 6 ALA A 92 ASP A 99 -1 O TYR A 95 N PHE A 37 SHEET 5 C 6 THR A 127 SER A 132 -1 O THR A 127 N TYR A 94 SHEET 6 C 6 GLY A 10 GLN A 13 1 N GLY A 10 O GLN A 128 SHEET 1 D 4 GLN B 3 GLY B 8 0 SHEET 2 D 4 LEU B 18 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 D 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 D 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 E 5 THR B 58 TYR B 60 0 SHEET 2 E 5 GLU B 46 ASN B 52 -1 N ALA B 50 O TYR B 59 SHEET 3 E 5 CYS B 33 GLN B 39 -1 N ARG B 38 O GLU B 46 SHEET 4 E 5 ALA B 92 ASP B 99 -1 O TYR B 95 N PHE B 37 SHEET 5 E 5 SER B 122 TRP B 123 -1 O SER B 122 N ALA B 98 SHEET 1 F 6 THR B 58 TYR B 60 0 SHEET 2 F 6 GLU B 46 ASN B 52 -1 N ALA B 50 O TYR B 59 SHEET 3 F 6 CYS B 33 GLN B 39 -1 N ARG B 38 O GLU B 46 SHEET 4 F 6 ALA B 92 ASP B 99 -1 O TYR B 95 N PHE B 37 SHEET 5 F 6 THR B 127 SER B 132 -1 O THR B 127 N TYR B 94 SHEET 6 F 6 GLY B 10 GLN B 13 1 N GLY B 10 O THR B 130 SHEET 1 G 3 THR L 43 ARG L 45 0 SHEET 2 G 3 THR L 51 TYR L 53 -1 O ASP L 52 N ASN L 44 SHEET 3 G 3 ILE L 58 ASN L 59 -1 O ILE L 58 N TYR L 53 SHEET 1 H 3 THR M 43 ARG M 45 0 SHEET 2 H 3 THR M 51 TYR M 53 -1 O ASP M 52 N ASN M 44 SHEET 3 H 3 ILE M 58 ASN M 59 -1 O ILE M 58 N TYR M 53 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.03 SSBOND 2 CYS A 33 CYS A 109 1555 1555 2.03 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 4 CYS B 33 CYS B 109 1555 1555 2.02 SSBOND 5 CYS L 6 CYS L 127 1555 1555 2.03 SSBOND 6 CYS L 30 CYS L 115 1555 1555 2.04 SSBOND 7 CYS L 64 CYS L 80 1555 1555 2.04 SSBOND 8 CYS L 76 CYS L 94 1555 1555 2.03 SSBOND 9 CYS M 6 CYS M 127 1555 1555 2.02 SSBOND 10 CYS M 30 CYS M 115 1555 1555 2.06 SSBOND 11 CYS M 64 CYS M 80 1555 1555 2.04 SSBOND 12 CYS M 76 CYS M 94 1555 1555 2.02 LINK OD1 ASP A 99 NA NA A 501 1555 1555 2.38 LINK O GLY A 119 NA NA A 501 1555 1555 2.35 LINK OD2 ASP A 121 NA NA A 501 1555 1555 2.43 LINK NA NA A 501 O HOH A 510 1555 1555 2.49 LINK NA NA A 501 O HOH A 537 1555 1555 2.39 LINK OD1 ASP B 99 NA NA B 502 1555 1555 2.29 LINK O GLY B 119 NA NA B 502 1555 1555 2.28 LINK OD2 ASP B 121 NA NA B 502 1555 1555 2.46 LINK NA NA B 502 O HOH B 511 1555 1555 2.40 LINK NA NA B 502 O HOH M 559 1555 1555 2.50 LINK OE1 GLU L 35 NA NA L 505 1555 1555 2.67 LINK O SER L 60 NA NA L 503 1555 1555 2.31 LINK O CYS L 64 NA NA L 503 1555 1555 2.57 LINK OG SER L 72 NA NA L 503 1555 1555 2.43 LINK O LYS L 73 NA NA L 503 1555 1555 2.37 LINK O1 FMT L 406 NA NA L 505 1555 1555 2.60 LINK NA NA L 503 O HOH L 515 1555 1555 2.49 LINK NA NA L 503 O HOH L 568 1555 1555 2.48 LINK NA NA L 505 O HOH L 526 1555 1555 2.27 LINK NA NA L 505 O HOH L 551 1555 1555 2.78 LINK O SER M 60 NA NA M 504 1555 1555 2.30 LINK O CYS M 64 NA NA M 504 1555 1555 2.44 LINK OG SER M 72 NA NA M 504 1555 1555 2.54 LINK O LYS M 73 NA NA M 504 1555 1555 2.25 LINK NA NA M 504 O HOH M 520 1555 1555 2.53 LINK NA NA M 504 O HOH M 533 1555 1555 2.46 CISPEP 1 GLY A 30 PRO A 31 0 0.23 CISPEP 2 GLY B 30 PRO B 31 0 0.26 SITE 1 AC1 6 ASP A 99 THR A 101 GLY A 119 ASP A 121 SITE 2 AC1 6 HOH A 510 HOH A 537 SITE 1 AC2 6 ASP B 99 THR B 101 GLY B 119 ASP B 121 SITE 2 AC2 6 HOH B 511 HOH M 559 SITE 1 AC3 6 SER L 60 CYS L 64 SER L 72 LYS L 73 SITE 2 AC3 6 HOH L 515 HOH L 568 SITE 1 AC4 6 SER M 60 CYS M 64 SER M 72 LYS M 73 SITE 2 AC4 6 HOH M 520 HOH M 533 SITE 1 AC5 6 SER A 105 GLU L 35 FMT L 406 HOH L 526 SITE 2 AC5 6 HOH L 550 HOH L 551 SITE 1 AC6 7 ALA A 6 TYR A 94 TYR A 95 CYS A 96 SITE 2 AC6 7 GLY A 124 GLY A 126 THR A 127 SITE 1 AC7 9 ALA B 6 TYR B 94 TYR B 95 CYS B 96 SITE 2 AC7 9 GLY B 124 GLN B 125 GLY B 126 THR B 127 SITE 3 AC7 9 HOH B 566 SITE 1 AC8 7 ASN M 65 GLY M 67 ARG M 68 THR M 69 SITE 2 AC8 7 SER M 72 HOH M 520 HOH M 533 SITE 1 AC9 2 HOH B 511 HOH M 543 SITE 1 BC1 6 ASN L 113 ARG L 114 HOH L 540 ARG M 5 SITE 2 BC1 6 CYS M 6 HOH M 511 SITE 1 BC2 7 GLU L 35 VAL L 109 ALA L 110 NA L 505 SITE 2 BC2 7 HOH L 551 HOH L 571 HOH L 576 CRYST1 67.123 69.375 113.231 90.00 90.00 90.00 P 21 21 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 0.014898 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008832 0.00000