HEADER SUGAR BINDING PROTEIN 06-AUG-09 3IKN TITLE CRYSTAL STRUCTURE OF GALACTOSE BOUND TRIMERIC HUMAN LUNG SURFACTANT TITLE 2 PROTEIN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: PULMONARY SURFACTANT-ASSOCIATED PROTEIN D; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 199-375; COMPND 5 SYNONYM: SP-D, PSP-D, LUNG SURFACTANT PROTEIN D; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: RECOMBINANT TRIMERIC FRAGMENT OF ALPHA HELICAL NECK COMPND 9 REGION PLUS CARBOHYDRATE RECOGNITION DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SFTPD, PSPD, SFTP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TRIMERIC RECOMBINANT FRAGMENT, NECK+CRD, COLLAGEN, DISULFIDE BOND, KEYWDS 2 EXTRACELLULAR MATRIX, GASEOUS EXCHANGE, GLYCOPROTEIN, HYDROXYLATION, KEYWDS 3 LECTIN, SECRETED, SURFACE FILM, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.SHRIVE,T.J.GREENHOUGH REVDAT 5 01-NOV-23 3IKN 1 REMARK REVDAT 4 10-NOV-21 3IKN 1 SEQADV HETSYN REVDAT 3 29-JUL-20 3IKN 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 19-FEB-14 3IKN 1 JRNL VERSN REVDAT 1 17-NOV-09 3IKN 0 JRNL AUTH A.K.SHRIVE,C.MARTIN,I.BURNS,J.M.PATERSON,J.D.MARTIN, JRNL AUTH 2 J.P.TOWNSEND,P.WATERS,H.W.CLARK,U.KISHORE,K.B.M.REID, JRNL AUTH 3 T.J.GREENHOUGH JRNL TITL STRUCTURAL CHARACTERISATION OF LIGAND-BINDING DETERMINANTS JRNL TITL 2 IN HUMAN LUNG SURFACTANT PROTEIN D: INFLUENCE OF ASP325 JRNL REF J.MOL.BIOL. V. 394 776 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19799916 JRNL DOI 10.1016/J.JMB.2009.09.057 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.K.SHRIVE,H.A.THARIA,P.STRONG,U.KISHORE,I.BURNS, REMARK 1 AUTH 2 P.J.RIZKALLAH,K.B.M.REID,T.J.GREENHOUGH REMARK 1 TITL HIGH-RESOLUTION STRUCTURAL INSIGHTS INTO LIGAND BINDING AND REMARK 1 TITL 2 IMMUNE CELL RECOGNITION BY HUMAN LUNG SURFACTANT PROTEIN D. REMARK 1 REF J.MOL.BIOL. V. 331 509 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12888356 REMARK 1 DOI 10.1016/S0022-2836(03)00761-7 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.86 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) (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 83548 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 SET) : 0.201 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 4192 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2954 REMARK 3 BIN FREE R VALUE : 0.3093 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 346 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 : 3483 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75800 REMARK 3 B22 (A**2) : -0.33300 REMARK 3 B33 (A**2) : 2.09100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.30200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 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 : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.049 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.584 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.910 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.851 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 44.29 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4_3.1.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83548 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 55.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11900 REMARK 200 R SYM FOR SHELL (I) : 0.11900 REMARK 200 FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS TO NATIVE REMARK 200 CRYSTALS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1PW9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, SITTING 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 54.29000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -161.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A 179 REMARK 465 SER A 180 REMARK 465 PRO A 181 REMARK 465 GLY A 182 REMARK 465 LEU A 183 REMARK 465 LYS A 184 REMARK 465 GLY A 185 REMARK 465 ASP A 186 REMARK 465 LYS A 187 REMARK 465 GLY A 188 REMARK 465 ILE A 189 REMARK 465 PRO A 190 REMARK 465 GLY A 191 REMARK 465 ASP A 192 REMARK 465 LYS A 193 REMARK 465 GLY A 194 REMARK 465 ALA A 195 REMARK 465 LYS A 196 REMARK 465 GLY A 197 REMARK 465 GLU A 198 REMARK 465 SER A 199 REMARK 465 GLY A 200 REMARK 465 LEU A 201 REMARK 465 PRO A 202 REMARK 465 ASP A 203 REMARK 465 GLY B 179 REMARK 465 SER B 180 REMARK 465 PRO B 181 REMARK 465 GLY B 182 REMARK 465 LEU B 183 REMARK 465 LYS B 184 REMARK 465 GLY B 185 REMARK 465 ASP B 186 REMARK 465 LYS B 187 REMARK 465 GLY B 188 REMARK 465 ILE B 189 REMARK 465 PRO B 190 REMARK 465 GLY B 191 REMARK 465 ASP B 192 REMARK 465 LYS B 193 REMARK 465 GLY B 194 REMARK 465 ALA B 195 REMARK 465 LYS B 196 REMARK 465 GLY B 197 REMARK 465 GLU B 198 REMARK 465 SER B 199 REMARK 465 GLY B 200 REMARK 465 LEU B 201 REMARK 465 PRO B 202 REMARK 465 ASP B 203 REMARK 465 GLY C 179 REMARK 465 SER C 180 REMARK 465 PRO C 181 REMARK 465 GLY C 182 REMARK 465 LEU C 183 REMARK 465 LYS C 184 REMARK 465 GLY C 185 REMARK 465 ASP C 186 REMARK 465 LYS C 187 REMARK 465 GLY C 188 REMARK 465 ILE C 189 REMARK 465 PRO C 190 REMARK 465 GLY C 191 REMARK 465 ASP C 192 REMARK 465 LYS C 193 REMARK 465 GLY C 194 REMARK 465 ALA C 195 REMARK 465 LYS C 196 REMARK 465 GLY C 197 REMARK 465 GLU C 198 REMARK 465 SER C 199 REMARK 465 GLY C 200 REMARK 465 LEU C 201 REMARK 465 PRO C 202 REMARK 465 ASP C 203 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 316 51.37 -143.89 REMARK 500 SER A 328 57.25 -155.13 REMARK 500 ASN B 316 53.76 -140.58 REMARK 500 SER B 328 41.01 -147.84 REMARK 500 ASN C 316 49.23 -141.53 REMARK 500 ASP C 324 52.40 39.65 REMARK 500 SER C 328 40.19 -146.02 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 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 38 O REMARK 620 2 ASP A 297 OD1 102.1 REMARK 620 3 ASP A 297 OD2 80.3 48.6 REMARK 620 4 GLU A 301 OE1 126.7 96.0 75.2 REMARK 620 5 GLU A 301 OE2 78.6 120.1 73.5 49.3 REMARK 620 6 ASP A 324 OD1 92.5 159.5 150.1 86.5 76.7 REMARK 620 7 GLU A 329 O 77.0 90.4 126.6 153.0 144.3 78.8 REMARK 620 8 ASP A 330 OD1 153.7 73.5 112.0 79.5 126.5 87.0 77.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 52 O REMARK 620 2 HOH A 144 O 74.7 REMARK 620 3 GLU A 301 OE1 76.3 93.1 REMARK 620 4 ASP A 330 OD1 102.0 171.2 78.1 REMARK 620 5 ASP A 330 OD2 81.1 137.0 115.1 48.7 REMARK 620 6 HOH A 364 O 136.7 76.6 73.6 101.5 140.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 80 O REMARK 620 2 GLU A 232 OE1 90.0 REMARK 620 3 HOH B 68 O 85.4 175.2 REMARK 620 4 GLU B 232 OE1 102.5 86.5 93.2 REMARK 620 5 GLU C 232 OE1 166.7 87.2 97.6 90.3 REMARK 620 6 HOH C 367 O 81.8 95.7 84.9 175.2 85.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 321 OE1 REMARK 620 2 ASN A 323 OD1 76.2 REMARK 620 3 GLU A 329 OE1 146.9 74.6 REMARK 620 4 ASN A 341 OD1 66.3 140.6 144.8 REMARK 620 5 ASP A 342 O 127.2 140.3 71.3 76.2 REMARK 620 6 ASP A 342 OD1 71.1 86.3 91.6 92.7 75.1 REMARK 620 7 GAL A 405 O2 75.3 75.0 111.3 83.8 136.7 144.6 REMARK 620 8 GAL A 405 O1 129.2 119.8 79.8 78.3 73.2 148.3 65.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 21 O REMARK 620 2 ASP B 297 OD1 100.0 REMARK 620 3 ASP B 297 OD2 83.3 48.0 REMARK 620 4 GLU B 301 OE1 130.0 100.8 77.9 REMARK 620 5 GLU B 301 OE2 81.1 118.5 71.6 49.0 REMARK 620 6 ASP B 324 OD1 93.6 160.6 148.6 80.5 77.0 REMARK 620 7 GLU B 329 O 75.1 92.0 130.2 148.0 144.2 78.1 REMARK 620 8 ASP B 330 OD1 149.5 71.8 108.9 80.5 129.0 89.5 75.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 44 O REMARK 620 2 HOH B 60 O 84.3 REMARK 620 3 HOH B 61 O 168.2 90.6 REMARK 620 4 HOH B 160 O 89.3 83.3 100.7 REMARK 620 5 GLU B 301 OE1 80.1 80.2 88.6 161.2 REMARK 620 6 ASP B 330 OD1 76.2 154.2 105.2 112.7 80.0 REMARK 620 7 ASP B 330 OD2 108.1 155.9 80.6 76.4 121.6 49.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 321 OE1 REMARK 620 2 ASN B 323 OD1 72.8 REMARK 620 3 GLU B 329 OE1 143.1 75.0 REMARK 620 4 ASN B 341 OD1 68.7 139.8 145.2 REMARK 620 5 ASP B 342 O 128.1 139.6 70.7 76.6 REMARK 620 6 ASP B 342 OD1 71.3 82.7 87.2 95.6 75.1 REMARK 620 7 GAL B 405 O2 76.1 76.7 113.3 83.1 136.8 145.4 REMARK 620 8 GAL B 405 O1 134.9 119.8 77.6 81.8 72.7 147.4 66.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 14 O REMARK 620 2 ASP C 297 OD1 99.5 REMARK 620 3 ASP C 297 OD2 81.3 47.5 REMARK 620 4 GLU C 301 OE1 128.6 98.5 76.4 REMARK 620 5 GLU C 301 OE2 80.1 120.2 74.0 49.4 REMARK 620 6 ASP C 324 OD1 94.0 159.3 151.4 85.0 77.4 REMARK 620 7 GLU C 329 O 77.1 89.2 126.8 150.8 145.4 78.6 REMARK 620 8 ASP C 330 OD1 152.8 72.3 108.4 78.6 126.7 88.6 77.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 18 O REMARK 620 2 HOH C 64 O 168.4 REMARK 620 3 HOH C 111 O 86.1 89.9 REMARK 620 4 GLU C 301 OE1 84.7 83.9 80.0 REMARK 620 5 ASP C 330 OD1 73.8 105.8 151.5 78.2 REMARK 620 6 ASP C 330 OD2 99.3 88.5 157.7 121.9 48.9 REMARK 620 7 HOH C 357 O 90.1 100.3 84.7 164.1 114.7 73.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 321 OE1 REMARK 620 2 ASN C 323 OD1 73.0 REMARK 620 3 GLU C 329 OE1 145.1 75.3 REMARK 620 4 ASN C 341 OD1 69.4 140.8 143.8 REMARK 620 5 ASP C 342 O 128.5 140.2 71.6 75.2 REMARK 620 6 ASP C 342 OD1 73.9 85.0 89.2 94.7 73.1 REMARK 620 7 GAL C 405 O1 133.4 120.4 76.2 80.4 72.2 145.0 REMARK 620 8 GAL C 405 O2 75.4 77.4 111.4 83.0 135.6 148.0 66.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PW9 RELATED DB: PDB REMARK 900 NATIVE TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D REMARK 900 RELATED ID: 1PWB RELATED DB: PDB REMARK 900 MALTOSE BOUND TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D REMARK 900 RELATED ID: 3IKP RELATED DB: PDB REMARK 900 INOSITOL PHOSPHATE BOUND TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D REMARK 900 RELATED ID: 3IKQ RELATED DB: PDB REMARK 900 ALPHA 1-2 MANNOBIOSE BOUND TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D REMARK 900 RELATED ID: 3IKR RELATED DB: PDB REMARK 900 ALPHA 1-4 MANNOBIOSE BOUND TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D DBREF 3IKN A 179 355 UNP P35247 SFTPD_HUMAN 199 375 DBREF 3IKN B 179 355 UNP P35247 SFTPD_HUMAN 199 375 DBREF 3IKN C 179 355 UNP P35247 SFTPD_HUMAN 199 375 SEQADV 3IKN SER A 180 UNP P35247 PRO 200 ENGINEERED MUTATION SEQADV 3IKN SER B 180 UNP P35247 PRO 200 ENGINEERED MUTATION SEQADV 3IKN SER C 180 UNP P35247 PRO 200 ENGINEERED MUTATION SEQRES 1 A 177 GLY SER PRO GLY LEU LYS GLY ASP LYS GLY ILE PRO GLY SEQRES 2 A 177 ASP LYS GLY ALA LYS GLY GLU SER GLY LEU PRO ASP VAL SEQRES 3 A 177 ALA SER LEU ARG GLN GLN VAL GLU ALA LEU GLN GLY GLN SEQRES 4 A 177 VAL GLN HIS LEU GLN ALA ALA PHE SER GLN TYR LYS LYS SEQRES 5 A 177 VAL GLU LEU PHE PRO ASN GLY GLN SER VAL GLY GLU LYS SEQRES 6 A 177 ILE PHE LYS THR ALA GLY PHE VAL LYS PRO PHE THR GLU SEQRES 7 A 177 ALA GLN LEU LEU CYS THR GLN ALA GLY GLY GLN LEU ALA SEQRES 8 A 177 SER PRO ARG SER ALA ALA GLU ASN ALA ALA LEU GLN GLN SEQRES 9 A 177 LEU VAL VAL ALA LYS ASN GLU ALA ALA PHE LEU SER MET SEQRES 10 A 177 THR ASP SER LYS THR GLU GLY LYS PHE THR TYR PRO THR SEQRES 11 A 177 GLY GLU SER LEU VAL TYR SER ASN TRP ALA PRO GLY GLU SEQRES 12 A 177 PRO ASN ASP ASP GLY GLY SER GLU ASP CYS VAL GLU ILE SEQRES 13 A 177 PHE THR ASN GLY LYS TRP ASN ASP ARG ALA CYS GLY GLU SEQRES 14 A 177 LYS ARG LEU VAL VAL CYS GLU PHE SEQRES 1 B 177 GLY SER PRO GLY LEU LYS GLY ASP LYS GLY ILE PRO GLY SEQRES 2 B 177 ASP LYS GLY ALA LYS GLY GLU SER GLY LEU PRO ASP VAL SEQRES 3 B 177 ALA SER LEU ARG GLN GLN VAL GLU ALA LEU GLN GLY GLN SEQRES 4 B 177 VAL GLN HIS LEU GLN ALA ALA PHE SER GLN TYR LYS LYS SEQRES 5 B 177 VAL GLU LEU PHE PRO ASN GLY GLN SER VAL GLY GLU LYS SEQRES 6 B 177 ILE PHE LYS THR ALA GLY PHE VAL LYS PRO PHE THR GLU SEQRES 7 B 177 ALA GLN LEU LEU CYS THR GLN ALA GLY GLY GLN LEU ALA SEQRES 8 B 177 SER PRO ARG SER ALA ALA GLU ASN ALA ALA LEU GLN GLN SEQRES 9 B 177 LEU VAL VAL ALA LYS ASN GLU ALA ALA PHE LEU SER MET SEQRES 10 B 177 THR ASP SER LYS THR GLU GLY LYS PHE THR TYR PRO THR SEQRES 11 B 177 GLY GLU SER LEU VAL TYR SER ASN TRP ALA PRO GLY GLU SEQRES 12 B 177 PRO ASN ASP ASP GLY GLY SER GLU ASP CYS VAL GLU ILE SEQRES 13 B 177 PHE THR ASN GLY LYS TRP ASN ASP ARG ALA CYS GLY GLU SEQRES 14 B 177 LYS ARG LEU VAL VAL CYS GLU PHE SEQRES 1 C 177 GLY SER PRO GLY LEU LYS GLY ASP LYS GLY ILE PRO GLY SEQRES 2 C 177 ASP LYS GLY ALA LYS GLY GLU SER GLY LEU PRO ASP VAL SEQRES 3 C 177 ALA SER LEU ARG GLN GLN VAL GLU ALA LEU GLN GLY GLN SEQRES 4 C 177 VAL GLN HIS LEU GLN ALA ALA PHE SER GLN TYR LYS LYS SEQRES 5 C 177 VAL GLU LEU PHE PRO ASN GLY GLN SER VAL GLY GLU LYS SEQRES 6 C 177 ILE PHE LYS THR ALA GLY PHE VAL LYS PRO PHE THR GLU SEQRES 7 C 177 ALA GLN LEU LEU CYS THR GLN ALA GLY GLY GLN LEU ALA SEQRES 8 C 177 SER PRO ARG SER ALA ALA GLU ASN ALA ALA LEU GLN GLN SEQRES 9 C 177 LEU VAL VAL ALA LYS ASN GLU ALA ALA PHE LEU SER MET SEQRES 10 C 177 THR ASP SER LYS THR GLU GLY LYS PHE THR TYR PRO THR SEQRES 11 C 177 GLY GLU SER LEU VAL TYR SER ASN TRP ALA PRO GLY GLU SEQRES 12 C 177 PRO ASN ASP ASP GLY GLY SER GLU ASP CYS VAL GLU ILE SEQRES 13 C 177 PHE THR ASN GLY LYS TRP ASN ASP ARG ALA CYS GLY GLU SEQRES 14 C 177 LYS ARG LEU VAL VAL CYS GLU PHE HET CA A 401 1 HET CA A 402 1 HET CA A 403 1 HET CA A 404 1 HET GAL A 405 12 HET CA B 401 1 HET CA B 402 1 HET CA B 403 1 HET GAL B 405 12 HET CA C 401 1 HET CA C 402 1 HET CA C 403 1 HET GAL C 405 12 HETNAM CA CALCIUM ION HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 4 CA 10(CA 2+) FORMUL 8 GAL 3(C6 H12 O6) FORMUL 17 HOH *492(H2 O) HELIX 1 1 VAL A 204 PHE A 234 1 31 HELIX 2 2 PHE A 254 ALA A 264 1 11 HELIX 3 3 SER A 273 ASN A 288 1 16 HELIX 4 4 ASP A 324 SER A 328 5 5 HELIX 5 5 VAL B 204 PHE B 234 1 31 HELIX 6 6 PHE B 254 ALA B 264 1 11 HELIX 7 7 SER B 273 ASN B 288 1 16 HELIX 8 8 ASP B 324 SER B 328 5 5 HELIX 9 9 VAL C 204 PHE C 234 1 31 HELIX 10 10 PHE C 254 ALA C 264 1 11 HELIX 11 11 SER C 273 ASN C 288 1 16 HELIX 12 12 ASP C 324 SER C 328 5 5 SHEET 1 A 4 GLY A 237 VAL A 240 0 SHEET 2 A 4 LYS A 243 PRO A 253 -1 O PHE A 245 N GLN A 238 SHEET 3 A 4 LYS A 348 PHE A 355 -1 O CYS A 353 N LYS A 246 SHEET 4 A 4 GLN A 267 LEU A 268 -1 N GLN A 267 O GLU A 354 SHEET 1 B 3 ALA A 291 PHE A 292 0 SHEET 2 B 3 CYS A 331 ILE A 334 -1 O ILE A 334 N ALA A 291 SHEET 3 B 3 TRP A 340 ARG A 343 -1 O ASN A 341 N GLU A 333 SHEET 1 C 4 GLY B 237 VAL B 240 0 SHEET 2 C 4 LYS B 243 PRO B 253 -1 O PHE B 245 N GLN B 238 SHEET 3 C 4 LYS B 348 PHE B 355 -1 O CYS B 353 N LYS B 246 SHEET 4 C 4 GLN B 267 LEU B 268 -1 N GLN B 267 O GLU B 354 SHEET 1 D 3 ALA B 291 PHE B 292 0 SHEET 2 D 3 CYS B 331 ILE B 334 -1 O ILE B 334 N ALA B 291 SHEET 3 D 3 TRP B 340 ARG B 343 -1 O ASN B 341 N GLU B 333 SHEET 1 E 4 GLY C 237 VAL C 240 0 SHEET 2 E 4 LYS C 243 PRO C 253 -1 O PHE C 245 N GLN C 238 SHEET 3 E 4 LYS C 348 PHE C 355 -1 O CYS C 353 N LYS C 246 SHEET 4 E 4 GLN C 267 LEU C 268 -1 N GLN C 267 O GLU C 354 SHEET 1 F 3 ALA C 291 PHE C 292 0 SHEET 2 F 3 CYS C 331 ILE C 334 -1 O ILE C 334 N ALA C 291 SHEET 3 F 3 TRP C 340 ARG C 343 -1 O ASN C 341 N GLU C 333 SSBOND 1 CYS A 261 CYS A 353 1555 1555 2.03 SSBOND 2 CYS A 331 CYS A 345 1555 1555 2.04 SSBOND 3 CYS B 261 CYS B 353 1555 1555 2.03 SSBOND 4 CYS B 331 CYS B 345 1555 1555 2.04 SSBOND 5 CYS C 261 CYS C 353 1555 1555 2.03 SSBOND 6 CYS C 331 CYS C 345 1555 1555 2.03 LINK O HOH A 38 CA CA A 402 1555 1555 2.57 LINK O HOH A 52 CA CA A 403 1555 1555 2.61 LINK O HOH A 80 CA CA A 404 1555 1555 2.66 LINK O HOH A 144 CA CA A 403 1555 1555 2.69 LINK OE1 GLU A 232 CA CA A 404 1555 1555 2.50 LINK OD1 ASP A 297 CA CA A 402 1555 1555 2.72 LINK OD2 ASP A 297 CA CA A 402 1555 1555 2.60 LINK OE1 GLU A 301 CA CA A 402 1555 1555 2.60 LINK OE2 GLU A 301 CA CA A 402 1555 1555 2.64 LINK OE1 GLU A 301 CA CA A 403 1555 1555 2.56 LINK OE1 GLU A 321 CA CA A 401 1555 1555 2.69 LINK OD1 ASN A 323 CA CA A 401 1555 1555 2.62 LINK OD1 ASP A 324 CA CA A 402 1555 1555 2.65 LINK OE1 GLU A 329 CA CA A 401 1555 1555 2.52 LINK O GLU A 329 CA CA A 402 1555 1555 2.57 LINK OD1 ASP A 330 CA CA A 402 1555 1555 2.55 LINK OD1 ASP A 330 CA CA A 403 1555 1555 2.67 LINK OD2 ASP A 330 CA CA A 403 1555 1555 2.64 LINK OD1 ASN A 341 CA CA A 401 1555 1555 2.56 LINK O ASP A 342 CA CA A 401 1555 1555 2.66 LINK OD1 ASP A 342 CA CA A 401 1555 1555 2.48 LINK O HOH A 364 CA CA A 403 1555 1555 2.67 LINK CA CA A 401 O2 GAL A 405 1555 1555 2.60 LINK CA CA A 401 O1 GAL A 405 1555 1555 2.67 LINK CA CA A 404 O HOH B 68 1555 1555 2.60 LINK CA CA A 404 OE1 GLU B 232 1555 1555 2.55 LINK CA CA A 404 OE1 GLU C 232 1555 1555 2.41 LINK CA CA A 404 O HOH C 367 1555 1555 2.61 LINK O HOH B 21 CA CA B 402 1555 1555 2.54 LINK O HOH B 44 CA CA B 403 1555 1555 2.62 LINK O HOH B 60 CA CA B 403 1555 1555 2.60 LINK O HOH B 61 CA CA B 403 1555 1555 2.72 LINK O HOH B 160 CA CA B 403 1555 1555 2.70 LINK OD1 ASP B 297 CA CA B 402 1555 1555 2.76 LINK OD2 ASP B 297 CA CA B 402 1555 1555 2.64 LINK OE1 GLU B 301 CA CA B 402 1555 1555 2.59 LINK OE2 GLU B 301 CA CA B 402 1555 1555 2.67 LINK OE1 GLU B 301 CA CA B 403 1555 1555 2.54 LINK OE1 GLU B 321 CA CA B 401 1555 1555 2.62 LINK OD1 ASN B 323 CA CA B 401 1555 1555 2.52 LINK OD1 ASP B 324 CA CA B 402 1555 1555 2.67 LINK OE1 GLU B 329 CA CA B 401 1555 1555 2.57 LINK O GLU B 329 CA CA B 402 1555 1555 2.53 LINK OD1 ASP B 330 CA CA B 402 1555 1555 2.54 LINK OD1 ASP B 330 CA CA B 403 1555 1555 2.62 LINK OD2 ASP B 330 CA CA B 403 1555 1555 2.62 LINK OD1 ASN B 341 CA CA B 401 1555 1555 2.48 LINK O ASP B 342 CA CA B 401 1555 1555 2.64 LINK OD1 ASP B 342 CA CA B 401 1555 1555 2.46 LINK CA CA B 401 O2 GAL B 405 1555 1555 2.59 LINK CA CA B 401 O1 GAL B 405 1555 1555 2.61 LINK O HOH C 14 CA CA C 402 1555 1555 2.55 LINK O HOH C 18 CA CA C 403 1555 1555 2.65 LINK O HOH C 64 CA CA C 403 1555 1555 2.68 LINK O HOH C 111 CA CA C 403 1555 1555 2.63 LINK OD1 ASP C 297 CA CA C 402 1555 1555 2.79 LINK OD2 ASP C 297 CA CA C 402 1555 1555 2.67 LINK OE1 GLU C 301 CA CA C 402 1555 1555 2.57 LINK OE2 GLU C 301 CA CA C 402 1555 1555 2.65 LINK OE1 GLU C 301 CA CA C 403 1555 1555 2.51 LINK OE1 GLU C 321 CA CA C 401 1555 1555 2.59 LINK OD1 ASN C 323 CA CA C 401 1555 1555 2.54 LINK OD1 ASP C 324 CA CA C 402 1555 1555 2.69 LINK OE1 GLU C 329 CA CA C 401 1555 1555 2.53 LINK O GLU C 329 CA CA C 402 1555 1555 2.52 LINK OD1 ASP C 330 CA CA C 402 1555 1555 2.53 LINK OD1 ASP C 330 CA CA C 403 1555 1555 2.61 LINK OD2 ASP C 330 CA CA C 403 1555 1555 2.68 LINK OD1 ASN C 341 CA CA C 401 1555 1555 2.50 LINK O ASP C 342 CA CA C 401 1555 1555 2.67 LINK OD1 ASP C 342 CA CA C 401 1555 1555 2.46 LINK O HOH C 357 CA CA C 403 1555 1555 2.75 LINK CA CA C 401 O1 GAL C 405 1555 1555 2.67 LINK CA CA C 401 O2 GAL C 405 1555 1555 2.54 CISPEP 1 PHE A 234 PRO A 235 0 0.20 CISPEP 2 GLU A 321 PRO A 322 0 -0.15 CISPEP 3 PHE B 234 PRO B 235 0 0.14 CISPEP 4 GLU B 321 PRO B 322 0 -0.19 CISPEP 5 PHE C 234 PRO C 235 0 0.23 CISPEP 6 GLU C 321 PRO C 322 0 -0.49 CRYST1 55.740 108.580 55.880 90.00 91.41 90.00 P 1 21 1 6 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 0.017940 0.000000 0.000442 0.00000 SCALE2 0.000000 0.009210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017901 0.00000