HEADER MEMBRANE PROTEIN 06-JAN-94 1VMO TITLE CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): TITLE 2 A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN TITLE 3 INTERNAL THREE-FOLD SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITELLINE MEMBRANE OUTER LAYER PROTEIN I; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMIZU,D.G.VASSYLYEV,S.KIDO,Y.DOI,K.MORIKAWA REVDAT 3 05-JUN-24 1VMO 1 REMARK REVDAT 2 24-FEB-09 1VMO 1 VERSN REVDAT 1 31-MAY-94 1VMO 0 JRNL AUTH T.SHIMIZU,D.G.VASSYLYEV,S.KIDO,Y.DOI,K.MORIKAWA JRNL TITL CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN JRNL TITL 2 I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY JRNL TITL 3 STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY. JRNL REF EMBO J. V. 13 1003 1994 JRNL REFN ISSN 0261-4189 JRNL PMID 8131734 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.SHIMIZU,K.MORIKAWA,S.KIDO,Y.DOI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC DATA OF REMARK 1 TITL 2 VITELLINE MEMBRANE OUTER LAYER PROTEIN 1 VMO1 REMARK 1 REF J.MOL.BIOL. V. 235 793 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.830 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) : 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 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: NULL REMARK 4 REMARK 4 1VMO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 31.21000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.07500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.07500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.21000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.25500 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: MONOMERIC 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 THR A 2 -72.61 -85.47 REMARK 500 SER A 41 69.43 -65.08 REMARK 500 THR A 48 -113.33 -132.61 REMARK 500 LEU A 58 -6.81 -54.03 REMARK 500 SER A 65 -108.82 -133.53 REMARK 500 THR A 81 -59.17 -135.41 REMARK 500 SER A 94 -138.77 -128.44 REMARK 500 ASP A 99 49.62 -81.09 REMARK 500 ASP A 100 90.52 -62.00 REMARK 500 THR A 101 41.87 -149.74 REMARK 500 GLU A 113 -0.94 83.19 REMARK 500 SER A 144 74.25 44.66 REMARK 500 THR B 2 -60.06 1.59 REMARK 500 THR B 48 -89.22 -91.46 REMARK 500 SER B 65 -115.28 -123.85 REMARK 500 THR B 81 -32.58 -141.78 REMARK 500 SER B 94 -137.57 -146.20 REMARK 500 ASP B 99 75.85 -68.74 REMARK 500 GLU B 113 5.12 83.70 REMARK 500 ASP B 119 46.25 -90.68 REMARK 500 CYS B 133 177.90 179.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE HAS NOT BEEN REPORTED. A PAPER DESCRIBING THE REMARK 999 SEQUENCE IS IN PREPARATION. DBREF 1VMO A 1 163 UNP P41366 VMO1_CHICK 21 183 DBREF 1VMO B 1 163 UNP P41366 VMO1_CHICK 21 183 SEQRES 1 A 163 ARG THR ARG GLU TYR THR SER VAL ILE THR VAL PRO ASN SEQRES 2 A 163 GLY GLY HIS TRP GLY LYS TRP GLY ILE ARG GLN PHE CYS SEQRES 3 A 163 HIS SER GLY TYR ALA ASN GLY PHE ALA LEU LYS VAL GLU SEQRES 4 A 163 PRO SER GLN PHE GLY ARG ASP ASP THR ALA LEU ASN GLY SEQRES 5 A 163 ILE ARG LEU ARG CYS LEU ASP GLY SER VAL ILE GLU SER SEQRES 6 A 163 LEU VAL GLY LYS TRP GLY THR TRP THR SER PHE LEU VAL SEQRES 7 A 163 CYS PRO THR GLY TYR LEU VAL SER PHE SER LEU ARG SER SEQRES 8 A 163 GLU LYS SER GLN GLY GLY GLY ASP ASP THR ALA ALA ASN SEQRES 9 A 163 ASN ILE GLN PHE ARG CYS SER ASP GLU ALA VAL LEU VAL SEQRES 10 A 163 GLY ASP GLY LEU SER TRP GLY ARG PHE GLY PRO TRP SER SEQRES 11 A 163 LYS ARG CYS LYS ILE CYS GLY LEU GLN THR LYS VAL GLU SEQRES 12 A 163 SER PRO GLN GLY LEU ARG ASP ASP THR ALA LEU ASN ASN SEQRES 13 A 163 VAL ARG PHE PHE CYS CYS LYS SEQRES 1 B 163 ARG THR ARG GLU TYR THR SER VAL ILE THR VAL PRO ASN SEQRES 2 B 163 GLY GLY HIS TRP GLY LYS TRP GLY ILE ARG GLN PHE CYS SEQRES 3 B 163 HIS SER GLY TYR ALA ASN GLY PHE ALA LEU LYS VAL GLU SEQRES 4 B 163 PRO SER GLN PHE GLY ARG ASP ASP THR ALA LEU ASN GLY SEQRES 5 B 163 ILE ARG LEU ARG CYS LEU ASP GLY SER VAL ILE GLU SER SEQRES 6 B 163 LEU VAL GLY LYS TRP GLY THR TRP THR SER PHE LEU VAL SEQRES 7 B 163 CYS PRO THR GLY TYR LEU VAL SER PHE SER LEU ARG SER SEQRES 8 B 163 GLU LYS SER GLN GLY GLY GLY ASP ASP THR ALA ALA ASN SEQRES 9 B 163 ASN ILE GLN PHE ARG CYS SER ASP GLU ALA VAL LEU VAL SEQRES 10 B 163 GLY ASP GLY LEU SER TRP GLY ARG PHE GLY PRO TRP SER SEQRES 11 B 163 LYS ARG CYS LYS ILE CYS GLY LEU GLN THR LYS VAL GLU SEQRES 12 B 163 SER PRO GLN GLY LEU ARG ASP ASP THR ALA LEU ASN ASN SEQRES 13 B 163 VAL ARG PHE PHE CYS CYS LYS FORMUL 3 HOH *144(H2 O) SHEET 1 S1A 4 SER A 61 ILE A 63 0 SHEET 2 S1A 4 GLY A 52 CYS A 57 -1 SHEET 3 S1A 4 ASN A 32 VAL A 38 -1 SHEET 4 S1A 4 THR A 72 THR A 74 -1 SHEET 1 S2A 4 SER A 61 ILE A 63 0 SHEET 2 S2A 4 GLY A 52 CYS A 57 -1 SHEET 3 S2A 4 ASN A 32 VAL A 38 -1 SHEET 4 S2A 4 LEU A 77 CYS A 79 -1 SHEET 1 S3A 4 ALA A 114 LEU A 116 0 SHEET 2 S3A 4 ASN A 105 CYS A 110 -1 SHEET 3 S3A 4 VAL A 85 SER A 91 -1 SHEET 4 S3A 4 ARG A 125 GLY A 127 -1 SHEET 1 S4A 4 SER A 7 ILE A 9 0 SHEET 2 S4A 4 ASN A 156 CYS A 161 -1 SHEET 3 S4A 4 CYS A 136 VAL A 142 -1 SHEET 4 S4A 4 LYS A 19 GLY A 21 -1 SHEET 1 S5A 4 SER A 7 ILE A 9 0 SHEET 2 S5A 4 ASN A 156 CYS A 161 -1 SHEET 3 S5A 4 CYS A 136 VAL A 142 -1 SHEET 4 S5A 4 GLN A 24 CYS A 26 -1 SHEET 1 S1B 4 SER B 61 ILE B 63 0 SHEET 2 S1B 4 GLY B 52 CYS B 57 -1 SHEET 3 S1B 4 ASN B 32 VAL B 38 -1 SHEET 4 S1B 4 THR B 72 THR B 74 -1 SHEET 1 S2B 4 SER B 61 ILE B 63 0 SHEET 2 S2B 4 GLY B 52 CYS B 57 -1 SHEET 3 S2B 4 ASN B 32 VAL B 38 -1 SHEET 4 S2B 4 LEU B 77 CYS B 79 -1 SHEET 1 S3B 4 ALA B 114 LEU B 116 0 SHEET 2 S3B 4 ASN B 105 CYS B 110 -1 SHEET 3 S3B 4 VAL B 85 SER B 91 -1 SHEET 4 S3B 4 ARG B 125 GLY B 127 -1 SHEET 1 S4B 4 SER B 7 ILE B 9 0 SHEET 2 S4B 4 ASN B 156 CYS B 161 -1 SHEET 3 S4B 4 CYS B 136 VAL B 142 -1 SHEET 4 S4B 4 LYS B 19 GLY B 21 -1 SHEET 1 S5B 4 SER B 7 ILE B 9 0 SHEET 2 S5B 4 ASN B 156 CYS B 161 -1 SHEET 3 S5B 4 CYS B 136 VAL B 142 -1 SHEET 4 S5B 4 GLN B 24 CYS B 26 -1 SSBOND 1 CYS A 26 CYS A 57 1555 1555 2.01 SSBOND 2 CYS A 79 CYS A 110 1555 1555 2.03 SSBOND 3 CYS A 133 CYS A 161 1555 1555 2.03 SSBOND 4 CYS A 136 CYS A 162 1555 1555 2.03 SSBOND 5 CYS B 26 CYS B 57 1555 1555 2.02 SSBOND 6 CYS B 79 CYS B 110 1555 1555 2.01 SSBOND 7 CYS B 133 CYS B 161 1555 1555 2.02 SSBOND 8 CYS B 136 CYS B 162 1555 1555 2.02 CRYST1 62.420 110.510 44.150 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 0.016021 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022650 0.00000 MTRIX1 1 0.994100 0.104960 0.027290 32.22300 1 MTRIX2 1 -0.107080 0.989840 0.093530 2.48600 1 MTRIX3 1 -0.017200 -0.095900 0.995240 12.49100 1