HEADER STRUCTURAL PROTEIN 17-APR-13 4K83 TITLE CRYSTAL STRUCTURE OF LV-RANASPUMIN (LV-RSN-1) FROM THE FOAM NEST OF TITLE 2 LEPTODACTYLUS VASTUS, ORTHORHOMBIC CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LV-RANASPUMIN (LV-RSN-1); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTODACTYLUS VASTUS; SOURCE 3 ORGANISM_COMMON: FROG; SOURCE 4 ORGANISM_TAXID: 326589; SOURCE 5 OTHER_DETAILS: FOAM NEST KEYWDS ALPHA-HELICAL, SURFACTANT PROTEIN, FOAM NEST, FROG, AMPHIBIAN, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.C.HISSA,G.A.BEZERRA,V.M.M.MELO,K.GRUBER REVDAT 3 20-SEP-23 4K83 1 REMARK REVDAT 2 24-JAN-18 4K83 1 AUTHOR REVDAT 1 05-MAR-14 4K83 0 JRNL AUTH D.CAVALCANTE HISSA,G.ARRUDA BEZERRA,R.BIRNER-GRUENBERGER, JRNL AUTH 2 L.PAULINO SILVA,I.USON,K.GRUBER,V.M.MACIEL MELO JRNL TITL UNIQUE CRYSTAL STRUCTURE OF A NOVEL SURFACTANT PROTEIN FROM JRNL TITL 2 THE FOAM NEST OF THE FROG LEPTODACTYLUS VASTUS. JRNL REF CHEMBIOCHEM V. 15 393 2014 JRNL REFN ISSN 1439-4227 JRNL PMID 24442854 JRNL DOI 10.1002/CBIC.201300726 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 20684 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1065 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 47.0465 - 3.4996 1.00 2654 119 0.1784 0.2132 REMARK 3 2 3.4996 - 2.7778 1.00 2509 124 0.2028 0.2643 REMARK 3 3 2.7778 - 2.4267 1.00 2460 127 0.2066 0.2389 REMARK 3 4 2.4267 - 2.2048 0.99 2431 150 0.2010 0.2487 REMARK 3 5 2.2048 - 2.0468 0.99 2396 156 0.2198 0.2744 REMARK 3 6 2.0468 - 1.9261 0.99 2393 125 0.2323 0.3149 REMARK 3 7 1.9261 - 1.8297 0.99 2396 137 0.2479 0.2951 REMARK 3 8 1.8297 - 1.7500 0.98 2380 127 0.2536 0.3203 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 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 : 0.007 1596 REMARK 3 ANGLE : 1.109 2149 REMARK 3 CHIRALITY : 0.073 265 REMARK 3 PLANARITY : 0.004 271 REMARK 3 DIHEDRAL : 12.593 619 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 4K83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-12 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9497 REMARK 200 MONOCHROMATOR : BARTELS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 51.359 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 25.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 43.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 26.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : 0.50000 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4K82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M SODIUM ACETATE, 28% PEG 3350, REMARK 280 PH 8.0, VAPOUR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 18.33100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.35850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.35850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.33100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.45000 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 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 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 LEU A 1 REMARK 465 LEU A 2 REMARK 465 GLU A 3 REMARK 465 GLY A 4 REMARK 465 PHE A 5 REMARK 465 LEU A 6 REMARK 465 VAL A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 GLY A 10 REMARK 465 VAL A 11 REMARK 465 PRO A 12 REMARK 465 SER A 216 REMARK 465 SER A 217 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 ASN A 214 O HOH A 499 2.08 REMARK 500 O HOH A 481 O HOH A 485 2.15 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 LEU A 82 -34.23 -159.09 REMARK 500 VAL A 145 -54.67 -122.64 REMARK 500 CYS A 146 38.81 -90.88 REMARK 500 VAL A 205 -60.78 -107.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K82 RELATED DB: PDB REMARK 900 LV-RANASPUMIN (LV-RSN-1) FROM THE FOAM NEST OF LEPTODACTYLUS VASTUS, REMARK 900 MONOCLINIC CRYSTAL FORM DBREF 4K83 A 1 217 PDB 4K83 4K83 1 217 SEQRES 1 A 217 LEU LEU GLU GLY PHE LEU VAL GLY GLY GLY VAL PRO GLY SEQRES 2 A 217 PRO GLY THR ALA CYS LEU THR LYS ALA LEU LYS ASP SER SEQRES 3 A 217 GLY ASP LEU LEU VAL GLU LEU ALA VAL ILE ILE CYS ALA SEQRES 4 A 217 TYR GLN ASN GLY LYS ASP LEU GLN GLU GLN ASP PHE LYS SEQRES 5 A 217 GLU LEU LYS GLU LEU LEU GLU ARG THR LEU GLU ARG ALA SEQRES 6 A 217 GLY CYS ALA LEU ASP ASP ILE VAL ALA ASP LEU GLY LEU SEQRES 7 A 217 GLU GLU LEU LEU GLY SER ILE GLY VAL SER THR GLY ASP SEQRES 8 A 217 ILE ILE GLN GLY LEU TYR LYS LEU LEU LYS GLU LEU LYS SEQRES 9 A 217 ILE ASP GLU THR VAL PHE ASN ALA VAL CYS ASP VAL THR SEQRES 10 A 217 LYS LYS MET LEU ASP ASN LYS CYS LEU PRO LYS ILE LEU SEQRES 11 A 217 GLN GLY ASP LEU VAL LYS PHE LEU LYS ASP LEU LYS TYR SEQRES 12 A 217 LYS VAL CYS ILE GLU GLY GLY ASP PRO GLU LEU ILE ILE SEQRES 13 A 217 LYS ASP LEU LYS ILE ILE LEU GLU ARG LEU PRO CYS VAL SEQRES 14 A 217 LEU GLY GLY VAL GLY LEU ASP ASP LEU PHE LYS ASN ILE SEQRES 15 A 217 PHE VAL LYS ASP GLY ILE LEU SER PHE GLU GLY ILE ALA SEQRES 16 A 217 LYS PRO LEU GLY ASP LEU LEU ILE LEU VAL LEU CYS PRO SEQRES 17 A 217 ASN VAL LYS ASN ILE ASN VAL SER SER FORMUL 2 HOH *204(H2 O) HELIX 1 1 GLY A 13 SER A 26 1 14 HELIX 2 2 GLY A 27 GLY A 43 1 17 HELIX 3 3 GLN A 47 ALA A 65 1 19 HELIX 4 4 ALA A 68 GLY A 77 1 10 HELIX 5 5 SER A 88 LEU A 103 1 16 HELIX 6 6 ASP A 106 ASN A 123 1 18 HELIX 7 7 CYS A 125 GLY A 132 1 8 HELIX 8 8 ASP A 133 VAL A 145 1 13 HELIX 9 9 ASP A 151 LEU A 166 1 16 HELIX 10 10 PRO A 167 GLY A 171 5 5 HELIX 11 11 GLY A 174 LYS A 180 1 7 HELIX 12 12 ALA A 195 VAL A 205 1 11 HELIX 13 13 VAL A 205 ILE A 213 1 9 SHEET 1 A 2 ILE A 182 LYS A 185 0 SHEET 2 A 2 ILE A 188 PHE A 191 -1 O ILE A 188 N LYS A 185 SSBOND 1 CYS A 18 CYS A 67 1555 1555 2.06 SSBOND 2 CYS A 38 CYS A 114 1555 1555 2.05 SSBOND 3 CYS A 125 CYS A 168 1555 1555 2.02 SSBOND 4 CYS A 146 CYS A 207 1555 1555 2.04 CISPEP 1 GLU A 79 GLU A 80 0 28.26 CISPEP 2 LEU A 81 LEU A 82 0 1.40 CRYST1 36.662 52.900 102.717 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 0.027276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009735 0.00000