HEADER SUGAR BINDING PROTEIN 26-AUG-16 5LSH TITLE HUMAN LYSOZYME IN COMPLEX WITH A TETRASACCHARIDE FRAGMENT OF THE O- TITLE 2 CHAIN OF LPS FROM KLEBSIELLA PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: 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: MUS MUSCULUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS LECTIN, COMPLEX, LPS, O-CHAIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,N.E.NIFANTIEV,V.KRYLOV,T.LUETTEKE,A.J.SCHEIDIG,H.-C.SIEBERT REVDAT 4 17-JAN-24 5LSH 1 HETSYN REVDAT 3 29-JUL-20 5LSH 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 27-DEC-17 5LSH 1 JRNL REVDAT 1 21-JUN-17 5LSH 0 JRNL AUTH R.ZHANG,L.WU,T.ECKERT,M.BURG-RODERFELD,M.A.ROJAS-MACIAS, JRNL AUTH 2 T.LUTTEKE,V.B.KRYLOV,D.A.ARGUNOV,A.DATTA,P.MARKART, JRNL AUTH 3 A.GUENTHER,B.NORDEN,R.SCHAUER,A.BHUNIA,M.A.ENANI,M.BILLETER, JRNL AUTH 4 A.J.SCHEIDIG,N.E.NIFANTIEV,H.C.SIEBERT JRNL TITL LYSOZYME'S LECTIN-LIKE CHARACTERISTICS FACILITATES ITS JRNL TITL 2 IMMUNE DEFENSE FUNCTION. JRNL REF Q. REV. BIOPHYS. V. 50 E9 2017 JRNL REFN ESSN 1469-8994 JRNL PMID 29233221 JRNL DOI 10.1017/S0033583517000075 REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 47421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2372 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 30.2778 - 2.7276 0.99 3076 162 0.1576 0.1694 REMARK 3 2 2.7276 - 2.1652 0.97 2873 152 0.1711 0.2038 REMARK 3 3 2.1652 - 1.8915 0.96 2831 151 0.1691 0.1982 REMARK 3 4 1.8915 - 1.7186 0.96 2784 146 0.1823 0.1879 REMARK 3 5 1.7186 - 1.5954 0.96 2778 146 0.1675 0.2237 REMARK 3 6 1.5954 - 1.5014 0.95 2742 145 0.1697 0.2077 REMARK 3 7 1.5014 - 1.4262 0.95 2758 142 0.1741 0.1955 REMARK 3 8 1.4262 - 1.3641 0.95 2735 144 0.1866 0.1949 REMARK 3 9 1.3641 - 1.3116 0.94 2694 143 0.1921 0.2198 REMARK 3 10 1.3116 - 1.2663 0.94 2673 141 0.1979 0.2224 REMARK 3 11 1.2663 - 1.2267 0.93 2664 140 0.2110 0.2383 REMARK 3 12 1.2267 - 1.1917 0.93 2670 141 0.2173 0.2489 REMARK 3 13 1.1917 - 1.1603 0.92 2625 138 0.2280 0.2689 REMARK 3 14 1.1603 - 1.1320 0.90 2560 135 0.2385 0.2698 REMARK 3 15 1.1320 - 1.1062 0.89 2528 133 0.2600 0.2714 REMARK 3 16 1.1062 - 1.0827 0.87 2479 130 0.3007 0.3480 REMARK 3 17 1.0827 - 1.0610 0.55 1579 83 0.3418 0.3208 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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 : 0.013 1288 REMARK 3 ANGLE : 1.569 1773 REMARK 3 CHIRALITY : 0.105 205 REMARK 3 PLANARITY : 0.009 220 REMARK 3 DIHEDRAL : 27.705 544 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 5LSH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200000941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47721 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.061 REMARK 200 RESOLUTION RANGE LOW (A) : 30.265 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1REX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M NACL, 25 MM NAOAC, PH 5.4, VAPOR REMARK 280 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 16.55400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.26550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.26550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.55400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.02000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 302 O HOH A 383 1.90 REMARK 500 O HOH A 303 O HOH A 339 1.93 REMARK 500 O HOH A 309 O HOH A 383 2.09 REMARK 500 NE2 GLN A 126 O HOH A 301 2.13 REMARK 500 O HOH A 309 O HOH A 340 2.15 REMARK 500 OE2 GLU A 35 O HOH A 302 2.15 REMARK 500 OG1 THR A 43 O HOH A 303 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 4 CD GLU A 4 OE2 0.071 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 CYS A 116 -37.62 -132.60 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 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 11 O REMARK 620 2 GLY A 127 O 57.2 REMARK 620 3 HOH A 448 O 58.5 8.3 REMARK 620 N 1 2 DBREF 5LSH A 1 130 UNP P61626 LYSC_HUMAN 19 148 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 ARG ASP PRO GLN SEQRES 9 A 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN SEQRES 10 A 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL HET TVG B 1 30 HET GLA B 2 22 HET GZL B 3 22 HET GLA B 4 22 HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET NA A 204 1 HETNAM TVG PROPYL BETA-D-GALACTOFURANOSIDE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM GZL BETA-D-GALACTOFURANOSE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN GZL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 TVG C9 H18 O6 FORMUL 2 GLA 2(C6 H12 O6) FORMUL 2 GZL C6 H12 O6 FORMUL 3 CL 3(CL 1-) FORMUL 6 NA NA 1+ FORMUL 7 HOH *160(H2 O) HELIX 1 AA1 GLU A 4 LEU A 15 1 12 HELIX 2 AA2 GLY A 19 ILE A 23 5 5 HELIX 3 AA3 SER A 24 GLY A 37 1 14 HELIX 4 AA4 SER A 80 GLN A 86 5 7 HELIX 5 AA5 ILE A 89 ARG A 101 1 13 HELIX 6 AA6 GLN A 104 ALA A 108 5 5 HELIX 7 AA7 TRP A 109 CYS A 116 1 8 HELIX 8 AA8 VAL A 121 VAL A 125 5 5 SHEET 1 AA1 3 THR A 43 TYR A 45 0 SHEET 2 AA1 3 THR A 52 TYR A 54 -1 O ASP A 53 N ASN A 44 SHEET 3 AA1 3 ILE A 59 ASN A 60 -1 O ILE A 59 N TYR A 54 SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.09 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.09 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.05 SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.05 LINK O3 ATVG B 1 C1 AGLA B 2 1555 1555 1.44 LINK O3 BTVG B 1 C1 BGLA B 2 1555 1555 1.43 LINK O3 AGLA B 2 C1 AGZL B 3 1555 1555 1.42 LINK O3 BGLA B 2 C1 BGZL B 3 1555 1555 1.42 LINK O3 AGZL B 3 C1 AGLA B 4 1555 1555 1.45 LINK O3 BGZL B 3 C1 BGLA B 4 1555 1555 1.43 LINK O THR A 11 NA NA A 204 1555 4456 2.95 LINK O GLY A 127 NA NA A 204 1555 1555 2.69 LINK NA NA A 204 O HOH A 448 1555 4556 2.80 CRYST1 33.108 56.040 60.531 90.00 90.00 90.00 P 21 21 21 4 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 0.030204 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016520 0.00000