HEADER HORMONE 29-MAY-09 3HMS TITLE CRYSTAL CRYSTAL STRUCTURE OF THE N-TERMINAL FRAGMENT (28-126) OF THE TITLE 2 HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR, ORTHORHOMBIC CRYSTAL TITLE 3 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOCYTE GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN: UNP RESIDUES 28-126; COMPND 5 SYNONYM: SCATTER FACTOR, SF, HEPATOPOEITIN-A, HEPATOCYTE GROWTH COMPND 6 FACTOR ALPHA CHAIN, HEPATOCYTE GROWTH FACTOR BETA CHAIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HGF, HPTA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B(DE); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-DUET1/TRX KEYWDS HGF/SF, HORMONE/GROWTH FACTOR, DISULFIDE BOND, GLYCOPROTEIN, GROWTH KEYWDS 2 FACTOR, KRINGLE, PYRROLIDONE CARBOXYLIC ACID, SERINE PROTEASE KEYWDS 3 HOMOLOG, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR W.D.TOLBERT REVDAT 3 06-SEP-23 3HMS 1 REMARK SEQADV REVDAT 2 01-SEP-10 3HMS 1 JRNL REVDAT 1 09-JUN-10 3HMS 0 JRNL AUTH W.D.TOLBERT,J.DAUGHERTY-HOLTROP,E.GHERARDI,G.VANDE WOUDE, JRNL AUTH 2 H.E.XU JRNL TITL STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM OF HEPATOCYTE JRNL TITL 2 GROWTH FACTOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 13264 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20624990 JRNL DOI 10.1073/PNAS.1005183107 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 469264.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 9610 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) : 0.202 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1010 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1329 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.02000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : 1.16000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.330 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.49 REMARK 3 BSOL : 72.20 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HMS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-04 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 : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9924 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 32.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : 0.40000 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1NK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM AMMONIUM SULFATE, 28-32% PEG REMARK 280 1000 OR 2000, 50 MM TRIS-HCL PH 8.0, 5% ISOPROPANOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 19.45500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.17500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.17500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.45500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.10500 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 GLY A 26 REMARK 465 SER A 27 REMARK 465 TYR A 28 REMARK 465 ALA A 29 REMARK 465 GLU A 30 REMARK 465 GLY A 31 REMARK 465 GLN A 32 REMARK 465 ARG A 33 REMARK 465 LYS A 34 REMARK 465 ARG A 35 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 96 CA - CB - SG ANGL. DEV. = 7.0 DEGREES 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 ASN A 77 12.96 50.52 REMARK 500 ASN A 77 12.17 50.56 REMARK 500 PRO A 81 28.42 -72.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NK1 RELATED DB: PDB REMARK 900 NK1 STRUCTURE REMARK 900 RELATED ID: 1GP9 RELATED DB: PDB REMARK 900 NK1 STRUCTURE REMARK 900 RELATED ID: 1GMN RELATED DB: PDB REMARK 900 NK1-HEPARIN COMPLEXES REMARK 900 RELATED ID: 1GMO RELATED DB: PDB REMARK 900 NK1-HEPARIN COMPLEXES REMARK 900 RELATED ID: 1BHT RELATED DB: PDB REMARK 900 NK1 STRUCTURE REMARK 900 RELATED ID: 2HGF RELATED DB: PDB REMARK 900 NMR N-TERMINAL DOMAIN STRUCTURE REMARK 900 RELATED ID: 2QJ2 RELATED DB: PDB REMARK 900 NK1 STRUCTURE REMARK 900 RELATED ID: 2QJ4 RELATED DB: PDB REMARK 900 MOUSE NK1 STRUCTURE REMARK 900 RELATED ID: 3HMR RELATED DB: PDB REMARK 900 MOUSE NK2 N-TERMINAL DOMAIN STRUCTURE REMARK 900 RELATED ID: 3HMT RELATED DB: PDB REMARK 900 NK2 N-TERMINAL DOMAIN STRUCTURE REMARK 900 RELATED ID: 3HN4 RELATED DB: PDB REMARK 900 NK2 FRAGMENT DBREF 3HMS A 28 126 UNP P14210 HGF_HUMAN 28 126 SEQADV 3HMS GLY A 26 UNP P14210 EXPRESSION TAG SEQADV 3HMS SER A 27 UNP P14210 EXPRESSION TAG SEQRES 1 A 101 GLY SER TYR ALA GLU GLY GLN ARG LYS ARG ARG ASN THR SEQRES 2 A 101 ILE HIS GLU PHE LYS LYS SER ALA LYS THR THR LEU ILE SEQRES 3 A 101 LYS ILE ASP PRO ALA LEU LYS ILE LYS THR LYS LYS VAL SEQRES 4 A 101 ASN THR ALA ASP GLN CYS ALA ASN ARG CYS THR ARG ASN SEQRES 5 A 101 LYS GLY LEU PRO PHE THR CYS LYS ALA PHE VAL PHE ASP SEQRES 6 A 101 LYS ALA ARG LYS GLN CYS LEU TRP PHE PRO PHE ASN SER SEQRES 7 A 101 MET SER SER GLY VAL LYS LYS GLU PHE GLY HIS GLU PHE SEQRES 8 A 101 ASP LEU TYR GLU ASN LYS ASP TYR ILE ARG HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *108(H2 O) HELIX 1 1 THR A 38 HIS A 40 5 3 HELIX 2 2 THR A 66 ASN A 77 1 12 HELIX 3 3 ASP A 123 ILE A 125 5 3 SHEET 1 A 5 PHE A 42 LYS A 52 0 SHEET 2 A 5 VAL A 108 ASN A 121 -1 O LYS A 109 N ILE A 51 SHEET 3 A 5 ALA A 86 ASP A 90 -1 N PHE A 87 O TYR A 119 SHEET 4 A 5 GLN A 95 PHE A 99 -1 O PHE A 99 N ALA A 86 SHEET 5 A 5 LYS A 60 LYS A 63 -1 N LYS A 60 O TRP A 98 SSBOND 1 CYS A 70 CYS A 96 1555 1555 2.03 SSBOND 2 CYS A 74 CYS A 84 1555 1555 2.05 SITE 1 AC1 5 ARG A 36 ASN A 37 SER A 105 HOH A1011 SITE 2 AC1 5 HOH A1085 CRYST1 38.910 42.210 52.350 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 0.025700 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019102 0.00000