HEADER SIGNALING PROTEIN 15-APR-09 2WG4 TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING TITLE 2 PROTEIN HIP AND SONIC HEDGEHOG WITHOUT CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SONIC HEDGEHOG PROTEIN N-PRODUCT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL SIGNALLING DOMAIN OF SHH, RESIDUES 40-191; COMPND 5 SYNONYM: SONIC HEDGEHOG SHH, SONIC HEDGEHOG PROTEIN, HHG-1, SHH; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HEDGEHOG-INTERACTING PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: C-TERMINAL DOMAIN OF HIP, RESIDUES 214-670; COMPND 11 SYNONYM: HHIP, HIP, HEDGEHOG-INTERACTING PROTEIN HIP; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HUMAN EMBRYONIC KIDNEY (HEK) 293T SOURCE 9 CELLS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HUMAN EMBRYONIC KIDNEY (HEK) 293T SOURCE 19 CELLS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PHLSEC KEYWDS AUTOCATALYTIC CLEAVAGE, PROTEASE, MEMBRANE, SECRETED, PALMITATE, KEYWDS 2 HYDROLASE, SIGNAL TRANSDUCTION, DEVELOPMENTAL PROTEIN, SIGNALING KEYWDS 3 PROTEIN, LIPOPROTEIN, DEVELOPMENT, GLYCOPROTEIN, CELL MEMBRANE, KEYWDS 4 DISULFIDE BOND, EGF-LIKE DOMAIN, HEDGEHOG SIGNALING EXPDTA X-RAY DIFFRACTION AUTHOR B.BISHOP,A.R.ARICESCU,K.HARLOS,C.A.O'CALLAGHAN,E.Y.JONES,C.SIEBOLD REVDAT 4 13-DEC-23 2WG4 1 REMARK LINK REVDAT 3 08-NOV-17 2WG4 1 SOURCE REVDAT 2 21-JUL-09 2WG4 1 JRNL REVDAT 1 30-JUN-09 2WG4 0 JRNL AUTH B.BISHOP,A.R.ARICESCU,K.HARLOS,C.A.O'CALLAGHAN,E.Y.JONES, JRNL AUTH 2 C.SIEBOLD JRNL TITL STRUCTURAL INSIGHTS INTO HEDGEHOG LIGAND SEQUESTRATION BY JRNL TITL 2 THE HUMAN HEDGEHOG-INTERACTING PROTEIN HIP JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 698 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19561611 JRNL DOI 10.1038/NSMB.1607 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 53.9 REMARK 3 NUMBER OF REFLECTIONS : 13824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 678 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 19.8426 - 5.3582 0.56 2767 124 0.2592 0.2962 REMARK 3 2 5.3582 - 4.2669 0.54 2638 137 0.1867 0.2556 REMARK 3 3 4.2669 - 3.7316 0.53 2623 124 0.2118 0.2621 REMARK 3 4 3.7316 - 3.3922 0.53 2559 149 0.2469 0.3255 REMARK 3 5 3.3922 - 3.1501 0.53 2559 144 0.2885 0.3413 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 : 0.32 REMARK 3 B_SOL : 25.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.12370 REMARK 3 B22 (A**2) : 3.12370 REMARK 3 B33 (A**2) : -6.24750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.002 4571 REMARK 3 ANGLE : 0.497 6151 REMARK 3 CHIRALITY : 0.035 662 REMARK 3 PLANARITY : 0.002 805 REMARK 3 DIHEDRAL : 13.825 1679 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 40:50) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1113 -21.4745 0.3391 REMARK 3 T TENSOR REMARK 3 T11: 0.5249 T22: 0.6279 REMARK 3 T33: 0.6035 T12: -0.0604 REMARK 3 T13: 0.0149 T23: 0.1655 REMARK 3 L TENSOR REMARK 3 L11: 5.7570 L22: 4.9871 REMARK 3 L33: 6.7105 L12: 1.6584 REMARK 3 L13: 3.0121 L23: -1.8752 REMARK 3 S TENSOR REMARK 3 S11: 0.4391 S12: -0.7427 S13: 0.6681 REMARK 3 S21: 0.3481 S22: -0.7234 S23: -0.9425 REMARK 3 S31: -0.2900 S32: 0.3868 S33: 0.1759 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 51:77) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3948 -32.5908 -19.9011 REMARK 3 T TENSOR REMARK 3 T11: 0.8003 T22: 0.8644 REMARK 3 T33: 0.4892 T12: -0.0192 REMARK 3 T13: 0.0328 T23: 0.1778 REMARK 3 L TENSOR REMARK 3 L11: 1.1092 L22: 4.5907 REMARK 3 L33: -0.1245 L12: -0.7545 REMARK 3 L13: 0.1406 L23: 0.9588 REMARK 3 S TENSOR REMARK 3 S11: 0.1527 S12: 0.3709 S13: -0.0955 REMARK 3 S21: -1.2523 S22: -0.1130 S23: -0.2085 REMARK 3 S31: -0.3475 S32: -0.1446 S33: -0.0434 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 78:129) REMARK 3 ORIGIN FOR THE GROUP (A): 27.2349 -34.5573 -9.9634 REMARK 3 T TENSOR REMARK 3 T11: 0.4072 T22: 1.0787 REMARK 3 T33: 1.0620 T12: -0.0037 REMARK 3 T13: 0.0970 T23: 0.1186 REMARK 3 L TENSOR REMARK 3 L11: -2.6950 L22: 2.5246 REMARK 3 L33: 2.1096 L12: -1.2965 REMARK 3 L13: -0.5643 L23: 0.8372 REMARK 3 S TENSOR REMARK 3 S11: 0.1532 S12: 0.7545 S13: -0.0703 REMARK 3 S21: -0.0577 S22: -0.0232 S23: -1.1118 REMARK 3 S31: 0.4045 S32: 0.8629 S33: -0.0679 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 130:188) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3017 -31.4994 -6.0051 REMARK 3 T TENSOR REMARK 3 T11: 0.4786 T22: 0.7240 REMARK 3 T33: 0.5801 T12: -0.0417 REMARK 3 T13: 0.0448 T23: 0.1745 REMARK 3 L TENSOR REMARK 3 L11: 2.5788 L22: 3.8240 REMARK 3 L33: 2.3506 L12: -1.2856 REMARK 3 L13: -0.7180 L23: 1.2506 REMARK 3 S TENSOR REMARK 3 S11: -0.3452 S12: -0.1642 S13: -0.4456 REMARK 3 S21: -0.1898 S22: 0.0536 S23: -0.6632 REMARK 3 S31: 0.1468 S32: 0.5107 S33: 0.3602 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 215:276) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8267 -44.3701 17.0235 REMARK 3 T TENSOR REMARK 3 T11: 0.4562 T22: 0.7003 REMARK 3 T33: 0.5949 T12: -0.0448 REMARK 3 T13: -0.0060 T23: 0.1023 REMARK 3 L TENSOR REMARK 3 L11: 1.7346 L22: 2.3923 REMARK 3 L33: 0.7836 L12: -0.6479 REMARK 3 L13: -0.2224 L23: -1.6822 REMARK 3 S TENSOR REMARK 3 S11: 0.1381 S12: 0.0380 S13: -0.5800 REMARK 3 S21: -0.1059 S22: -0.0030 S23: 0.4404 REMARK 3 S31: 0.2460 S32: -0.4005 S33: -0.1529 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 277:442) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5251 -33.7637 12.5131 REMARK 3 T TENSOR REMARK 3 T11: 0.4034 T22: 0.5947 REMARK 3 T33: 0.4227 T12: -0.0047 REMARK 3 T13: -0.0376 T23: 0.0983 REMARK 3 L TENSOR REMARK 3 L11: 3.1406 L22: 1.9325 REMARK 3 L33: 2.2350 L12: 0.2272 REMARK 3 L13: -0.2133 L23: -0.6904 REMARK 3 S TENSOR REMARK 3 S11: -0.1428 S12: -0.0612 S13: 0.0771 REMARK 3 S21: 0.0818 S22: 0.0125 S23: -0.0818 REMARK 3 S31: -0.0662 S32: 0.2437 S33: 0.1025 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 443:530) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0938 -44.6176 29.9903 REMARK 3 T TENSOR REMARK 3 T11: 0.4465 T22: 0.8468 REMARK 3 T33: 0.5577 T12: 0.0337 REMARK 3 T13: -0.0596 T23: 0.1365 REMARK 3 L TENSOR REMARK 3 L11: 2.0658 L22: -0.2398 REMARK 3 L33: 1.2913 L12: 0.0839 REMARK 3 L13: -0.5072 L23: -0.7907 REMARK 3 S TENSOR REMARK 3 S11: 0.1104 S12: -0.6509 S13: -0.0015 REMARK 3 S21: 0.0621 S22: 0.0046 S23: 0.2030 REMARK 3 S31: 0.0910 S32: 0.2721 S33: -0.1013 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 531:637) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8388 -34.3769 22.3161 REMARK 3 T TENSOR REMARK 3 T11: 0.5698 T22: 0.7207 REMARK 3 T33: 0.5062 T12: -0.0311 REMARK 3 T13: 0.0185 T23: 0.0597 REMARK 3 L TENSOR REMARK 3 L11: 1.9330 L22: 2.1701 REMARK 3 L33: 0.6281 L12: -0.0856 REMARK 3 L13: 0.6306 L23: -1.5368 REMARK 3 S TENSOR REMARK 3 S11: 0.1042 S12: -0.4678 S13: -0.2025 REMARK 3 S21: -0.1417 S22: 0.1662 S23: 0.5404 REMARK 3 S31: -0.0684 S32: -0.3142 S33: -0.2097 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN B AND RESID 638:666) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9440 4.1008 -6.2016 REMARK 3 T TENSOR REMARK 3 T11: 1.0457 T22: 0.5114 REMARK 3 T33: 0.9893 T12: 0.1409 REMARK 3 T13: -0.0352 T23: -0.0523 REMARK 3 L TENSOR REMARK 3 L11: 7.2019 L22: 3.1623 REMARK 3 L33: 3.0328 L12: -6.9671 REMARK 3 L13: -1.4008 L23: -1.6476 REMARK 3 S TENSOR REMARK 3 S11: 1.1144 S12: -1.4527 S13: -0.6254 REMARK 3 S21: -3.0351 S22: -0.4690 S23: 1.7427 REMARK 3 S31: 0.0642 S32: 0.7669 S33: -0.5332 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 2WG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-09. REMARK 100 THE DEPOSITION ID IS D_1290039480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.89 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13878 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.21000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 ENTRIES 1VHH AND 2WFT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH 4.6 0.5 M REMARK 280 POTASSIUM THIOCYANATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 114.63067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.31533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.31533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 114.63067 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.7 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 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 GLU A 90 REMARK 465 GLU A 91 REMARK 465 ASN A 92 REMARK 465 THR A 93 REMARK 465 GLY A 94 REMARK 465 ASN A 190 REMARK 465 SER A 191 REMARK 465 VAL A 192 REMARK 465 ALA A 193 REMARK 465 ALA A 194 REMARK 465 HIS B 214 REMARK 465 GLY B 278 REMARK 465 GLY B 279 REMARK 465 GLU B 308 REMARK 465 ARG B 309 REMARK 465 TRP B 310 REMARK 465 ALA B 311 REMARK 465 ILE B 312 REMARK 465 GLY B 313 REMARK 465 PRO B 314 REMARK 465 GLY B 457 REMARK 465 LYS B 458 REMARK 465 ASN B 459 REMARK 465 GLY B 538 REMARK 465 THR B 539 REMARK 465 SER B 540 REMARK 465 GLY B 541 REMARK 465 SER B 542 REMARK 465 CYS B 543 REMARK 465 ARG B 544 REMARK 465 GLY B 545 REMARK 465 TYR B 546 REMARK 465 PHE B 547 REMARK 465 SER B 548 REMARK 465 GLY B 549 REMARK 465 SER B 568 REMARK 465 LYS B 569 REMARK 465 SER B 570 REMARK 465 MET B 571 REMARK 465 THR B 572 REMARK 465 GLN B 573 REMARK 465 THR B 574 REMARK 465 GLU B 667 REMARK 465 GLN B 668 REMARK 465 VAL B 669 REMARK 465 ASP B 670 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 LYS B 277 CG CD CE NZ REMARK 470 ARG B 460 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 651 CG CD NE CZ NH1 NH2 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 51 46.05 -77.94 REMARK 500 LYS A 55 31.83 -92.00 REMARK 500 ALA A 59 -111.40 -103.34 REMARK 500 THR A 68 -163.89 -106.32 REMARK 500 TYR A 81 42.03 -96.44 REMARK 500 ASP A 132 129.23 -179.27 REMARK 500 HIS A 134 -2.41 63.17 REMARK 500 TRP A 173 116.04 -165.04 REMARK 500 TYR A 176 74.19 -68.93 REMARK 500 ALA A 188 -159.30 -111.94 REMARK 500 ASN B 306 -165.93 -163.64 REMARK 500 HIS B 317 -168.78 -170.81 REMARK 500 HIS B 430 -74.75 -147.28 REMARK 500 SER B 461 129.21 177.95 REMARK 500 PHE B 486 -179.85 -61.85 REMARK 500 SER B 487 -79.60 -107.09 REMARK 500 ASN B 488 -67.80 -129.64 REMARK 500 PRO B 490 -142.64 -64.47 REMARK 500 LEU B 491 121.90 164.17 REMARK 500 GLN B 523 -156.37 -91.09 REMARK 500 THR B 527 -40.66 68.57 REMARK 500 PRO B 591 155.37 -49.81 REMARK 500 ARG B 610 -79.05 -65.50 REMARK 500 LEU B 611 60.57 -109.12 REMARK 500 PRO B 619 -5.23 -56.73 REMARK 500 VAL B 650 -72.23 -132.17 REMARK 500 PRO B 652 94.19 -51.85 REMARK 500 LYS B 658 -175.11 -66.21 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 A1190 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 141 NE2 REMARK 620 2 ASP A 148 OD1 115.4 REMARK 620 3 HIS A 183 ND1 106.9 107.0 REMARK 620 4 ASP B 383 OD2 90.2 125.4 110.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1667 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 410 O REMARK 620 2 ASN B 412 O 83.5 REMARK 620 3 ASP B 473 OD1 70.9 126.7 REMARK 620 4 TYR B 474 O 131.2 79.9 83.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1667 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1668 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1669 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1670 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WFX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING REMARK 900 PROTEIN HIP AND SONIC HEDGEHOG IN THE PRESENCE OF CALCIUM REMARK 900 RELATED ID: 2WFT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN HIP ECTODOMAIN REMARK 900 RELATED ID: 1VHH RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: SONIC HEDGEHOG; CHAIN: NULL; DOMAIN: AMINO- REMARK 900 TERMINAL DOMAIN (RESIDUES 34 - 195); SYNONYM: HHG-1, VHH-1; REMARK 900 ENGINEERED: YES REMARK 900 RELATED ID: 2WFQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL SIGNALLING DOMAIN OF HUMAN DHH REMARK 900 WITHOUT CALCIUM REMARK 900 RELATED ID: 2WFR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL SIGNALLING DOMAIN OF HUMAN DHH REMARK 900 WITH CALCIUM REMARK 900 RELATED ID: 2WG3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING REMARK 900 PROTEIN HIP AND DESERT HEDGEHOG WITHOUT CALCIUM DBREF 2WG4 A 40 191 UNP Q62226 SHH_MOUSE 40 191 DBREF 2WG4 B 214 670 UNP Q96QV1 HHIP_HUMAN 214 670 SEQRES 1 A 155 LEU THR PRO LEU ALA TYR LYS GLN PHE ILE PRO ASN VAL SEQRES 2 A 155 ALA GLU LYS THR LEU GLY ALA SER GLY ARG TYR GLU GLY SEQRES 3 A 155 LYS ILE THR ARG ASN SER GLU ARG PHE LYS GLU LEU THR SEQRES 4 A 155 PRO ASN TYR ASN PRO ASP ILE ILE PHE LYS ASP GLU GLU SEQRES 5 A 155 ASN THR GLY ALA ASP ARG LEU MET THR GLN ARG CYS LYS SEQRES 6 A 155 ASP LYS LEU ASN ALA LEU ALA ILE SER VAL MET ASN GLN SEQRES 7 A 155 TRP PRO GLY VAL LYS LEU ARG VAL THR GLU GLY TRP ASP SEQRES 8 A 155 GLU ASP GLY HIS HIS SER GLU GLU SER LEU HIS TYR GLU SEQRES 9 A 155 GLY ARG ALA VAL ASP ILE THR THR SER ASP ARG ASP ARG SEQRES 10 A 155 SER LYS TYR GLY MET LEU ALA ARG LEU ALA VAL GLU ALA SEQRES 11 A 155 GLY PHE ASP TRP VAL TYR TYR GLU SER LYS ALA HIS ILE SEQRES 12 A 155 HIS CYS SER VAL LYS ALA GLU ASN SER VAL ALA ALA SEQRES 1 B 457 HIS ASN CYS PHE CYS ILE GLN GLU VAL VAL SER GLY LEU SEQRES 2 B 457 ARG GLN PRO VAL GLY ALA LEU HIS SER GLY ASP GLY SER SEQRES 3 B 457 GLN ARG LEU PHE ILE LEU GLU LYS GLU GLY TYR VAL LYS SEQRES 4 B 457 ILE LEU THR PRO GLU GLY GLU ILE PHE LYS GLU PRO TYR SEQRES 5 B 457 LEU ASP ILE HIS LYS LEU VAL GLN SER GLY ILE LYS GLY SEQRES 6 B 457 GLY ASP GLU ARG GLY LEU LEU SER LEU ALA PHE HIS PRO SEQRES 7 B 457 ASN TYR LYS LYS ASN GLY LYS LEU TYR VAL SER TYR THR SEQRES 8 B 457 THR ASN GLN GLU ARG TRP ALA ILE GLY PRO HIS ASP HIS SEQRES 9 B 457 ILE LEU ARG VAL VAL GLU TYR THR VAL SER ARG LYS ASN SEQRES 10 B 457 PRO HIS GLN VAL ASP LEU ARG THR ALA ARG VAL PHE LEU SEQRES 11 B 457 GLU VAL ALA GLU LEU HIS ARG LYS HIS LEU GLY GLY GLN SEQRES 12 B 457 LEU LEU PHE GLY PRO ASP GLY PHE LEU TYR ILE ILE LEU SEQRES 13 B 457 GLY ASP GLY MET ILE THR LEU ASP ASP MET GLU GLU MET SEQRES 14 B 457 ASP GLY LEU SER ASP PHE THR GLY SER VAL LEU ARG LEU SEQRES 15 B 457 ASP VAL ASP THR ASP MET CYS ASN VAL PRO TYR SER ILE SEQRES 16 B 457 PRO ARG SER ASN PRO HIS PHE ASN SER THR ASN GLN PRO SEQRES 17 B 457 PRO GLU VAL PHE ALA HIS GLY LEU HIS ASP PRO GLY ARG SEQRES 18 B 457 CYS ALA VAL ASP ARG HIS PRO THR ASP ILE ASN ILE ASN SEQRES 19 B 457 LEU THR ILE LEU CYS SER ASP SER ASN GLY LYS ASN ARG SEQRES 20 B 457 SER SER ALA ARG ILE LEU GLN ILE ILE LYS GLY LYS ASP SEQRES 21 B 457 TYR GLU SER GLU PRO SER LEU LEU GLU PHE LYS PRO PHE SEQRES 22 B 457 SER ASN GLY PRO LEU VAL GLY GLY PHE VAL TYR ARG GLY SEQRES 23 B 457 CYS GLN SER GLU ARG LEU TYR GLY SER TYR VAL PHE GLY SEQRES 24 B 457 ASP ARG ASN GLY ASN PHE LEU THR LEU GLN GLN SER PRO SEQRES 25 B 457 VAL THR LYS GLN TRP GLN GLU LYS PRO LEU CYS LEU GLY SEQRES 26 B 457 THR SER GLY SER CYS ARG GLY TYR PHE SER GLY HIS ILE SEQRES 27 B 457 LEU GLY PHE GLY GLU ASP GLU LEU GLY GLU VAL TYR ILE SEQRES 28 B 457 LEU SER SER SER LYS SER MET THR GLN THR HIS ASN GLY SEQRES 29 B 457 LYS LEU TYR LYS ILE VAL ASP PRO LYS ARG PRO LEU MET SEQRES 30 B 457 PRO GLU GLU CYS ARG ALA THR VAL GLN PRO ALA GLN THR SEQRES 31 B 457 LEU THR SER GLU CYS SER ARG LEU CYS ARG ASN GLY TYR SEQRES 32 B 457 CYS THR PRO THR GLY LYS CYS CYS CYS SER PRO GLY TRP SEQRES 33 B 457 GLU GLY ASP PHE CYS ARG THR ALA LYS CYS GLU PRO ALA SEQRES 34 B 457 CYS ARG HIS GLY GLY VAL CYS VAL ARG PRO ASN LYS CYS SEQRES 35 B 457 LEU CYS LYS LYS GLY TYR LEU GLY PRO GLN CYS GLU GLN SEQRES 36 B 457 VAL ASP HET ZN A1190 1 HET NA B1667 1 HET NA B1668 1 HET NA B1669 1 HET NA B1670 1 HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 3 ZN ZN 2+ FORMUL 4 NA 4(NA 1+) HELIX 1 1 SER A 71 LEU A 77 5 7 HELIX 2 2 THR A 100 TRP A 118 1 19 HELIX 3 3 SER A 139 GLY A 144 5 6 HELIX 4 4 LYS A 158 ALA A 169 1 12 HELIX 5 5 ASN B 292 GLY B 297 1 6 HELIX 6 6 THR B 375 MET B 382 1 8 HELIX 7 7 SER B 606 LEU B 611 1 6 SHEET 1 AA 6 PHE A 48 ILE A 49 0 SHEET 2 AA 6 TRP A 173 TYR A 175 -1 O VAL A 174 N ILE A 49 SHEET 3 AA 6 ILE A 182 SER A 185 -1 O HIS A 183 N TYR A 175 SHEET 4 AA 6 ALA A 146 THR A 151 -1 O VAL A 147 N CYS A 184 SHEET 5 AA 6 LEU A 123 GLU A 127 -1 O ARG A 124 N THR A 150 SHEET 6 AA 6 ILE A 85 PHE A 87 1 O ILE A 86 N VAL A 125 SHEET 1 AB 2 THR A 78 PRO A 79 0 SHEET 2 AB 2 LEU A 98 MET A 99 -1 O MET A 99 N THR A 78 SHEET 1 BA 4 CYS B 218 VAL B 223 0 SHEET 2 BA 4 LYS B 578 VAL B 583 -1 O LEU B 579 N VAL B 222 SHEET 3 BA 4 VAL B 562 SER B 566 -1 O VAL B 562 N ILE B 582 SHEET 4 BA 4 ILE B 551 GLU B 556 -1 N LEU B 552 O LEU B 565 SHEET 1 BB 4 PRO B 229 LEU B 233 0 SHEET 2 BB 4 LEU B 242 GLU B 246 -1 O PHE B 243 N LEU B 233 SHEET 3 BB 4 TYR B 250 LEU B 254 -1 O TYR B 250 N GLU B 246 SHEET 4 BB 4 LEU B 266 ASP B 267 -1 O LEU B 266 N VAL B 251 SHEET 1 BC 4 LEU B 284 PHE B 289 0 SHEET 2 BC 4 LYS B 298 THR B 305 -1 O TYR B 300 N ALA B 288 SHEET 3 BC 4 HIS B 317 VAL B 326 -1 O ILE B 318 N THR B 305 SHEET 4 BC 4 VAL B 334 GLU B 347 -1 N ASP B 335 O THR B 325 SHEET 1 BD 4 GLY B 354 PHE B 359 0 SHEET 2 BD 4 LEU B 365 LEU B 369 -1 O TYR B 366 N LEU B 358 SHEET 3 BD 4 SER B 391 LEU B 395 -1 O SER B 391 N LEU B 369 SHEET 4 BD 4 VAL B 424 HIS B 427 -1 N PHE B 425 O VAL B 392 SHEET 1 BE 4 ALA B 436 ASP B 438 0 SHEET 2 BE 4 LEU B 448 ASP B 454 -1 O THR B 449 N ASP B 438 SHEET 3 BE 4 SER B 462 ILE B 468 -1 O SER B 462 N ASP B 454 SHEET 4 BE 4 LEU B 481 PHE B 483 -1 O LEU B 481 N ILE B 465 SHEET 1 BF 4 GLY B 493 VAL B 496 0 SHEET 2 BF 4 TYR B 509 GLY B 512 -1 O VAL B 510 N PHE B 495 SHEET 3 BF 4 PHE B 518 GLN B 522 -1 O LEU B 519 N PHE B 511 SHEET 4 BF 4 GLN B 531 LEU B 535 -1 O GLN B 531 N GLN B 522 SHEET 1 BG 2 GLY B 615 CYS B 617 0 SHEET 2 BG 2 CYS B 623 CYS B 625 -1 O CYS B 624 N TYR B 616 SHEET 1 BH 2 TRP B 629 GLU B 630 0 SHEET 2 BH 2 THR B 636 ALA B 637 -1 O THR B 636 N GLU B 630 SSBOND 1 CYS B 216 CYS B 536 1555 1555 2.03 SSBOND 2 CYS B 402 CYS B 624 1555 1555 2.03 SSBOND 3 CYS B 435 CYS B 452 1555 1555 2.03 SSBOND 4 CYS B 500 CYS B 594 1555 1555 2.03 SSBOND 5 CYS B 608 CYS B 617 1555 1555 2.03 SSBOND 6 CYS B 612 CYS B 623 1555 1555 2.03 SSBOND 7 CYS B 625 CYS B 634 1555 1555 2.03 SSBOND 8 CYS B 639 CYS B 649 1555 1555 2.03 SSBOND 9 CYS B 643 CYS B 655 1555 1555 2.03 SSBOND 10 CYS B 657 CYS B 666 1555 1555 2.03 LINK NE2 HIS A 141 ZN ZN A1190 1555 1555 2.01 LINK OD1 ASP A 148 ZN ZN A1190 1555 1555 2.05 LINK ND1 HIS A 183 ZN ZN A1190 1555 1555 2.01 LINK ZN ZN A1190 OD2 ASP B 383 1555 1555 2.06 LINK O ARG B 410 NA NA B1667 1555 1555 2.51 LINK O ASN B 412 NA NA B1667 1555 1555 2.47 LINK OD1 ASP B 473 NA NA B1667 1555 1555 2.44 LINK O TYR B 474 NA NA B1667 1555 1555 2.53 CISPEP 1 ILE A 49 PRO A 50 0 2.32 CISPEP 2 GLU B 640 PRO B 641 0 -0.91 SITE 1 AC1 4 HIS A 141 ASP A 148 HIS A 183 ASP B 383 SITE 1 AC2 5 ARG B 410 SER B 411 ASN B 412 ASP B 473 SITE 2 AC2 5 TYR B 474 SITE 1 AC3 3 PRO B 441 ASP B 443 ILE B 446 SITE 1 AC4 3 SER B 286 LEU B 287 LEU B 357 SITE 1 AC5 3 HIS B 269 VAL B 272 GLN B 273 CRYST1 88.055 88.055 171.946 90.00 90.00 120.00 P 32 2 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 0.011357 0.006557 0.000000 0.00000 SCALE2 0.000000 0.013113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005816 0.00000