PDB Short entry for 3LN2 HEADER HYDROLASE 01-FEB-10 3LN2 TITLE CRYSTAL STRUCTURE OF A CHARGE ENGINEERED HUMAN LYSOZYME VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LYZ, LZM; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BJ5464; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRS416-GAL1 KEYWDS HUMAN LYSOZYME, HYDROLASE, CHARGE ENGINEERED HUMAN LYSOZYME, PROTEIN KEYWDS 2 ENGINEERING, ANTIMICROBIAL, BACTERIOLYTIC, SURFACE MUTATION, KEYWDS 3 AMYLOID, AMYLOIDOSIS, BACTERIOLYTIC ENZYME, DISEASE MUTATION, KEYWDS 4 DISULFIDE BOND, GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR A.GILL,T.C.SCANLON,K.E.GRISWOLD REVDAT 4 06-SEP-23 3LN2 1 REMARK REVDAT 3 13-OCT-21 3LN2 1 SEQADV REVDAT 2 23-MAR-11 3LN2 1 JRNL REVDAT 1 16-FEB-11 3LN2 0 JRNL AUTH A.GILL,T.C.SCANLON,D.C.OSIPOVITCH,D.R.MADDEN,K.E.GRISWOLD JRNL TITL CRYSTAL STRUCTURE OF A CHARGE ENGINEERED HUMAN LYSOZYME JRNL TITL 2 HAVING ENHANCED BACTERICIDAL ACTIVITY. JRNL REF PLOS ONE V. 6 16788 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21408218 JRNL DOI 10.1371/JOURNAL.PONE.0016788 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19848 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8600 - 3.8892 1.00 2826 175 0.1731 0.1941 REMARK 3 2 3.8892 - 3.0907 1.00 2730 142 0.1755 0.2287 REMARK 3 3 3.0907 - 2.7011 1.00 2696 135 0.1942 0.2452 REMARK 3 4 2.7011 - 2.4547 1.00 2673 138 0.1865 0.2240 REMARK 3 5 2.4547 - 2.2790 1.00 2604 195 0.1689 0.2164 REMARK 3 6 2.2790 - 2.1448 1.00 2687 114 0.1577 0.2143 REMARK 3 7 2.1448 - 2.0375 0.98 2599 134 0.1769 0.2299 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 40.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 1.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.72410 REMARK 3 B22 (A**2) : -2.98450 REMARK 3 B33 (A**2) : -2.73960 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2100 REMARK 3 ANGLE : 1.014 2832 REMARK 3 CHIRALITY : 0.076 292 REMARK 3 PLANARITY : 0.004 374 REMARK 3 DIHEDRAL : 15.322 742 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.3 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) : 1.54 REMARK 200 MONOCHROMATOR : XENOCS FOX-2D MULTILAYER MIRRORS REMARK 200 OPTICS : XENOCS FOX-2D MULTILAYER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 19.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 9.490 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.490 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.5_2 REMARK 200 STARTING MODEL: PDB ENTRY 1LZS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM NA-ACETATE, 1.25M NACL, PH 4.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 21.21050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.53850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.89750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.53850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.21050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.89750 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, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 13 NZ REMARK 480 LYS A 33 NZ REMARK 480 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 13 CE NZ REMARK 480 LYS B 69 CG CD CE NZ REMARK 480 GLN B 126 CD OE1 NE2 DBREF 3LN2 A 1 130 UNP P61626 LYSC_HUMAN 19 148 DBREF 3LN2 B 1 130 UNP P61626 LYSC_HUMAN 19 148 SEQADV 3LN2 ASP A 101 UNP P61626 ARG 119 ENGINEERED MUTATION SEQADV 3LN2 HIS A 115 UNP P61626 ARG 133 ENGINEERED MUTATION SEQADV 3LN2 ASP B 101 UNP P61626 ARG 119 ENGINEERED MUTATION SEQADV 3LN2 HIS B 115 UNP P61626 ARG 133 ENGINEERED MUTATION SEQRES 1 A 130 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS SEQRES 2 A 130 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA SEQRES 3 A 130 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN SEQRES 4 A 130 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR SEQRES 5 A 130 ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS SEQRES 6 A 130 ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA CYS HIS SEQRES 7 A 130 LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP SEQRES 8 A 130 ALA VAL ALA CYS ALA LYS ARG VAL VAL ASP ASP PRO GLN SEQRES 9 A 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN HIS CYS GLN SEQRES 10 A 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL 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 ASP ASP PRO GLN SEQRES 9 B 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN HIS CYS GLN SEQRES 10 B 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL FORMUL 3 HOH *237(H2 O) HELIX 1 1 GLU A 4 LEU A 15 1 12 HELIX 2 2 GLY A 19 ILE A 23 5 5 HELIX 3 3 SER A 24 GLY A 37 1 14 HELIX 4 4 SER A 80 GLN A 86 5 7 HELIX 5 5 ILE A 89 ASP A 101 1 13 HELIX 6 6 GLN A 104 ALA A 108 5 5 HELIX 7 7 TRP A 109 CYS A 116 1 8 HELIX 8 8 VAL A 121 VAL A 125 5 5 HELIX 9 9 GLU B 4 LEU B 15 1 12 HELIX 10 10 GLY B 19 ILE B 23 5 5 HELIX 11 11 SER B 24 GLY B 37 1 14 HELIX 12 12 SER B 80 GLN B 86 5 7 HELIX 13 13 ILE B 89 ASP B 101 1 13 HELIX 14 14 GLN B 104 ALA B 108 5 5 HELIX 15 15 TRP B 109 CYS B 116 1 8 HELIX 16 16 VAL B 121 VAL B 125 5 5 SHEET 1 A 3 THR A 43 ASN A 46 0 SHEET 2 A 3 SER A 51 TYR A 54 -1 O SER A 51 N ASN A 46 SHEET 3 A 3 ILE A 59 ASN A 60 -1 O ILE A 59 N TYR A 54 SHEET 1 B 3 THR B 43 ASN B 46 0 SHEET 2 B 3 SER B 51 TYR B 54 -1 O SER B 51 N ASN B 46 SHEET 3 B 3 ILE B 59 ASN B 60 -1 O ILE B 59 N TYR B 54 SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.08 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.04 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.05 SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.04 SSBOND 5 CYS B 6 CYS B 128 1555 1555 2.08 SSBOND 6 CYS B 30 CYS B 116 1555 1555 2.02 SSBOND 7 CYS B 65 CYS B 81 1555 1555 2.05 SSBOND 8 CYS B 77 CYS B 95 1555 1555 2.06 CRYST1 42.421 63.795 111.077 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 0.023573 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009003 0.00000