HEADER GLYCOPROTEIN 26-NOV-97 1BIK TITLE X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIKUNIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN II,78 - 133; COMPND 5 SYNONYM: MINGIN, URINARY TRYPSIN INHIBITOR, HI30, TRYPSTATIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 SECRETION: URINE KEYWDS GLYCOPROTEIN, BIKUNIN, TRYPSTATIN, URINARY TRYPSIN INHIBITOR, URONIC- KEYWDS 2 ACID-RICH PROTEIN, SERINE PROTEASE INHIBITOR (KUNITZ TYPE), KEYWDS 3 GLYCOSYLATED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,P.D.CARR,J.M.GUSS,D.L.OLLIS REVDAT 6 20-NOV-24 1BIK 1 REMARK REVDAT 5 02-AUG-23 1BIK 1 HETSYN REVDAT 4 29-JUL-20 1BIK 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 1BIK 1 VERSN REVDAT 2 24-FEB-09 1BIK 1 VERSN REVDAT 1 16-MAR-99 1BIK 0 JRNL AUTH Y.XU,P.D.CARR,J.M.GUSS,D.L.OLLIS JRNL TITL THE CRYSTAL STRUCTURE OF BIKUNIN FROM THE JRNL TITL 2 INTER-ALPHA-INHIBITOR COMPLEX: A SERINE PROTEASE INHIBITOR JRNL TITL 3 WITH TWO KUNITZ DOMAINS. JRNL REF J.MOL.BIOL. V. 276 955 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9566199 JRNL DOI 10.1006/JMBI.1997.1582 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 7511 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) : 0.205 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 783 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 696 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 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 : 827 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 33 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.635 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.25 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.389 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : WATER.PARM REMARK 3 PARAMETER FILE 3 : SO4.PARM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : WATER.TOPO REMARK 3 TOPOLOGY FILE 3 : SO4.TOPO REMARK 3 TOPOLOGY FILE 4 : GLA_NEW.TOPO REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BIK 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_1000171799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: C-TERMINAL DOMAIN OF PDB ENTRY 1KNT REMARK 200 REMARK 200 REMARK: NON IDENTICAL RESIDUES TRUNCATED TO THE CB POSITION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.45000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.65000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.65000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.17500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.17500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.45000 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 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 ALA A 1 REMARK 465 VAL A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 GLU A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 GLN A 14 REMARK 465 LEU A 15 REMARK 465 VAL A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 VAL A 19 REMARK 465 THR A 20 REMARK 465 LYS A 21 REMARK 465 LYS A 22 REMARK 465 GLU A 23 REMARK 465 ASP A 24 REMARK 465 PRO A 135 REMARK 465 GLY A 136 REMARK 465 ASP A 137 REMARK 465 GLY A 138 REMARK 465 ASP A 139 REMARK 465 GLU A 140 REMARK 465 GLU A 141 REMARK 465 LEU A 142 REMARK 465 LEU A 143 REMARK 465 ARG A 144 REMARK 465 PHE A 145 REMARK 465 SER A 146 REMARK 465 ASN A 147 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 GLN A 27 CG CD OE1 NE2 REMARK 470 LYS A 126 CG CD CE NZ DBREF 1BIK A 1 147 UNP P02760 AMBP_HUMAN 206 352 SEQRES 1 A 147 ALA VAL LEU PRO GLN GLU GLU GLU GLY SER GLY GLY GLY SEQRES 2 A 147 GLN LEU VAL THR GLU VAL THR LYS LYS GLU ASP SER CYS SEQRES 3 A 147 GLN LEU GLY TYR SER ALA GLY PRO CYS MET GLY MET THR SEQRES 4 A 147 SER ARG TYR PHE TYR ASN GLY THR SER MET ALA CYS GLU SEQRES 5 A 147 THR PHE GLN TYR GLY GLY CYS MET GLY ASN GLY ASN ASN SEQRES 6 A 147 PHE VAL THR GLU LYS GLU CYS LEU GLN THR CYS ARG THR SEQRES 7 A 147 VAL ALA ALA CYS ASN LEU PRO ILE VAL ARG GLY PRO CYS SEQRES 8 A 147 ARG ALA PHE ILE GLN LEU TRP ALA PHE ASP ALA VAL LYS SEQRES 9 A 147 GLY LYS CYS VAL LEU PHE PRO TYR GLY GLY CYS GLN GLY SEQRES 10 A 147 ASN GLY ASN LYS PHE TYR SER GLU LYS GLU CYS ARG GLU SEQRES 11 A 147 TYR CYS GLY VAL PRO GLY ASP GLY ASP GLU GLU LEU LEU SEQRES 12 A 147 ARG PHE SER ASN MODRES 1BIK ASN A 45 ASN GLYCOSYLATION SITE HET NAG A 148 14 HET SO4 A 149 5 HET SO4 A 150 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *33(H2 O) HELIX 1 1 GLU A 69 CYS A 76 1 8 HELIX 2 2 VAL A 79 ASN A 83 5 5 HELIX 3 3 GLU A 125 CYS A 132 1 8 SHEET 1 A 2 THR A 39 ASN A 45 0 SHEET 2 A 2 ALA A 50 TYR A 56 -1 N TYR A 56 O THR A 39 SHEET 1 B 2 ILE A 95 ASP A 101 0 SHEET 2 B 2 LYS A 106 TYR A 112 -1 N TYR A 112 O ILE A 95 SSBOND 1 CYS A 26 CYS A 76 1555 1555 2.02 SSBOND 2 CYS A 35 CYS A 59 1555 1555 2.01 SSBOND 3 CYS A 51 CYS A 72 1555 1555 2.03 SSBOND 4 CYS A 82 CYS A 132 1555 1555 2.02 SSBOND 5 CYS A 91 CYS A 115 1555 1555 2.02 SSBOND 6 CYS A 107 CYS A 128 1555 1555 2.03 LINK ND2 ASN A 45 C1 NAG A 148 1555 1555 1.45 CRYST1 55.300 55.300 146.900 90.00 90.00 90.00 P 41 21 2 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 0.018083 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006807 0.00000