HEADER SIGNALLING PROTEIN 03-OCT-95 1VHH TITLE A POTENTIAL CATALYTIC SITE WITHIN THE AMINO-TERMINAL SIGNALLING DOMAIN TITLE 2 OF SONIC HEDGEHOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: SONIC HEDGEHOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HHG-1, VHH-1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: POTENTIAL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS SIGNALLING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.M.T.HALL,J.A.PORTER,P.A.BEACHY,D.J.LEAHY REVDAT 4 14-FEB-24 1VHH 1 REMARK LINK REVDAT 3 24-FEB-09 1VHH 1 VERSN REVDAT 2 01-APR-03 1VHH 1 JRNL REVDAT 1 29-JAN-96 1VHH 0 JRNL AUTH T.M.HALL,J.A.PORTER,P.A.BEACHY,D.J.LEAHY JRNL TITL A POTENTIAL CATALYTIC SITE REVEALED BY THE 1.7-A CRYSTAL JRNL TITL 2 STRUCTURE OF THE AMINO-TERMINAL SIGNALLING DOMAIN OF SONIC JRNL TITL 3 HEDGEHOG. JRNL REF NATURE V. 378 212 1995 JRNL REFN ISSN 0028-0836 JRNL PMID 7477329 JRNL DOI 10.1038/378212A0 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 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) (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 14783 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) : 0.191 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 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 : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.53 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.968 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.42 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.385 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 1VHH 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_1000177035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686, 0.9792, 0.9793, 0.9879 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 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 26.85000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.50000 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 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 450 REMARK 450 SOURCE REMARK 450 THE AMINO-TERMINAL DOMAIN OF MURINE SONIC HEDGEHOG WAS REMARK 450 EXPRESSED AS A GLUTATHIONE S-TRANSFERASE FUSION PROTEIN REMARK 450 USING THE PGEX2T VECTOR. THE FUSION PROTEIN WAS CLEAVED REMARK 450 WITH THROMBIN TO RELEASE THE SONIC HEDGEHOG FRAGMENT. 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 ARG A 34 REMARK 465 ARG A 35 REMARK 465 HIS A 36 REMARK 465 PRO A 37 REMARK 465 LYS A 38 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 HE2 HIS A 141 ZN ZN A 400 1.12 REMARK 500 HD1 HIS A 183 ZN ZN A 400 1.20 REMARK 500 O ARG A 62 HH22 ARG A 145 1.58 REMARK 500 O HOH A 233 H1 HOH A 235 1.58 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 LYS A 46 -2.78 75.49 REMARK 500 ALA A 59 -118.25 -104.31 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 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 141 NE2 REMARK 620 2 ASP A 148 OD1 106.0 REMARK 620 3 HIS A 183 ND1 112.0 112.2 REMARK 620 4 HOH A 201 O 111.1 116.3 99.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZN1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 DBREF 1VHH A 34 195 UNP Q62226 SHH_MOUSE 34 195 SEQRES 1 A 162 ARG ARG HIS PRO LYS LYS LEU THR PRO LEU ALA TYR LYS SEQRES 2 A 162 GLN PHE ILE PRO ASN VAL ALA GLU LYS THR LEU GLY ALA SEQRES 3 A 162 SER GLY ARG TYR GLU GLY LYS ILE THR ARG ASN SER GLU SEQRES 4 A 162 ARG PHE LYS GLU LEU THR PRO ASN TYR ASN PRO ASP ILE SEQRES 5 A 162 ILE PHE LYS ASP GLU GLU ASN THR GLY ALA ASP ARG LEU SEQRES 6 A 162 MET THR GLN ARG CYS LYS ASP LYS LEU ASN ALA LEU ALA SEQRES 7 A 162 ILE SER VAL MET ASN GLN TRP PRO GLY VAL LYS LEU ARG SEQRES 8 A 162 VAL THR GLU GLY TRP ASP GLU ASP GLY HIS HIS SER GLU SEQRES 9 A 162 GLU SER LEU HIS TYR GLU GLY ARG ALA VAL ASP ILE THR SEQRES 10 A 162 THR SER ASP ARG ASP ARG SER LYS TYR GLY MET LEU ALA SEQRES 11 A 162 ARG LEU ALA VAL GLU ALA GLY PHE ASP TRP VAL TYR TYR SEQRES 12 A 162 GLU SER LYS ALA HIS ILE HIS CYS SER VAL LYS ALA GLU SEQRES 13 A 162 ASN SER VAL ALA ALA LYS HET ZN A 400 1 HET SO4 A 401 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *120(H2 O) HELIX 1 1 GLU A 72 GLU A 76 5 5 HELIX 2 2 ALA A 95 ARG A 97 5 3 HELIX 3 3 GLN A 101 GLN A 117 1 17 HELIX 4 4 LEU A 140 GLU A 143 5 4 HELIX 5 5 ARG A 156 GLU A 168 5 13 HELIX 6 6 GLU A 189 VAL A 192 1 4 SHEET 1 A 5 ILE A 85 PHE A 87 0 SHEET 2 A 5 LEU A 123 GLU A 127 1 N LEU A 123 O ILE A 86 SHEET 3 A 5 ALA A 146 THR A 151 -1 N THR A 150 O ARG A 124 SHEET 4 A 5 ILE A 182 SER A 185 -1 N CYS A 184 O VAL A 147 SHEET 5 A 5 TRP A 173 TYR A 175 -1 N TYR A 175 O HIS A 183 LINK NE2 HIS A 141 ZN ZN A 400 1555 1555 2.06 LINK OD1 ASP A 148 ZN ZN A 400 1555 1555 1.97 LINK ND1 HIS A 183 ZN ZN A 400 1555 1555 2.08 LINK O HOH A 201 ZN ZN A 400 1555 1555 2.05 CISPEP 1 ILE A 49 PRO A 50 0 0.03 SITE 1 ZN1 4 HIS A 141 ASP A 148 HIS A 183 HOH A 201 SITE 1 AC1 6 HIS A 141 ASP A 148 GLU A 177 HIS A 183 SITE 2 AC1 6 LYS A 195 HOH A 201 SITE 1 AC2 8 ARG A 62 LYS A 88 ARG A 124 THR A 126 SITE 2 AC2 8 ARG A 154 ARG A 156 HOH A 221 HOH A 225 CRYST1 53.700 79.000 35.400 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 0.018622 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028249 0.00000