10 20 30 40 50 60 70 80 1SFP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SPERMADHESIN 24-JUN-97 1SFP
TITLE CRYSTAL STRUCTURE OF ACIDIC SEMINAL FLUID PROTEIN (ASFP) AT TITLE 2 1.9 A RESOLUTION: A BOVINE POLYPEPTIDE FROM THE TITLE 3 SPERMADHESIN FAMILY
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASFP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACIDIC SEMINAL PROTEIN; COMPND 5 OTHER_DETAILS: ASFP
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 SECRETION: SEMINAL PLASMA
KEYWDS SPERMADHESIN, BOVINE SEMINAL PLASMA PROTEIN, ACIDIC SEMINAL KEYWDS 2 FLUID PROTEIN, ASFP, CUB DOMAIN, X-RAY CRYSTAL STRUCTURE, KEYWDS 3 GROWTH FACTOR
EXPDTA X-RAY DIFFRACTION
AUTHOR M.J.ROMAO,I.KOLLN,J.M.DIAS,A.L.CARVALHO,A.ROMERO,P.F.VARELA, AUTHOR 2 L.SANZ,E.TOPFER-PETERSEN,J.J.CALVETE
REVDAT 2 24-FEB-09 1SFP 1 VERSN REVDAT 1 24-JUN-98 1SFP 0
JRNL AUTH A.ROMERO,M.J.ROMAO,P.F.VARELA,I.KOLLN,J.M.DIAS, JRNL AUTH 2 A.L.CARVALHO,L.SANZ,E.TOPFER-PETERSEN,J.J.CALVETE JRNL TITL THE CRYSTAL STRUCTURES OF TWO SPERMADHESINS REVEAL JRNL TITL 2 THE CUB DOMAIN FOLD. JRNL REF NAT.STRUCT.BIOL. V. 4 783 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9334740 JRNL DOI 10.1038/NSB1097-783
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.173 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8231 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.145 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6477 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 884 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 948.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3839 REMARK 3 NUMBER OF RESTRAINTS : 3634 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.022 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.348 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.014 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.119 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1SFP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8773 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXL-96 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 4.7, REMARK 280 POLYETHYLENEGLYCOL 4000, 10% DIOXANE
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 20.77500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.77500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.22000 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: DIMERIC 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 TRP A 3
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 28 CE NZ
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 ARG A 83 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 180 DISTANCE = 6.57 ANGSTROMS
DBREF 1SFP A 1 114 UNP P29392 ASFP_BOVIN 21 134
SEQRES 1 A 114 MET ASP TRP LEU PRO ARG ASN THR ASN CYS GLY GLY ILE SEQRES 2 A 114 LEU LYS GLU GLU SER GLY VAL ILE ALA THR TYR TYR GLY SEQRES 3 A 114 PRO LYS THR ASN CYS VAL TRP THR ILE GLN MET PRO PRO SEQRES 4 A 114 GLU TYR HIS VAL ARG VAL SER ILE GLN TYR LEU GLN LEU SEQRES 5 A 114 ASN CYS ASN LYS GLU SER LEU GLU ILE ILE ASP GLY LEU SEQRES 6 A 114 PRO GLY SER PRO VAL LEU GLY LYS ILE CYS GLU GLY SER SEQRES 7 A 114 LEU MET ASP TYR ARG SER SER GLY SER ILE MET THR VAL SEQRES 8 A 114 LYS TYR ILE ARG GLU PRO GLU HIS PRO ALA SER PHE TYR SEQRES 9 A 114 GLU VAL LEU TYR PHE GLN ASP PRO GLN ALA
FORMUL 2 HOH *74(H2 O)
SHEET 1 A 5 GLY A 12 LEU A 14 0 SHEET 2 A 5 ASN A 30 GLN A 36 1 N THR A 34 O GLY A 12 SHEET 3 A 5 ILE A 88 ARG A 95 -1 N TYR A 93 O CYS A 31 SHEET 4 A 5 GLU A 57 ILE A 62 -1 N ILE A 62 O THR A 90 SHEET 5 A 5 VAL A 70 ILE A 74 -1 N ILE A 74 O LEU A 59 SHEET 1 B 4 SER A 18 ALA A 22 0 SHEET 2 B 4 GLU A 105 ASP A 111 -1 N TYR A 108 O GLY A 19 SHEET 3 B 4 HIS A 42 ILE A 47 -1 N SER A 46 O LEU A 107 SHEET 4 B 4 MET A 80 ARG A 83 -1 N TYR A 82 O VAL A 45 SHEET 1 C 2 TYR A 49 GLN A 51 0 SHEET 2 C 2 GLU A 76 SER A 78 -1 N GLY A 77 O LEU A 50
SSBOND 1 CYS A 10 CYS A 31 1555 1555 2.05 SSBOND 2 CYS A 54 CYS A 75 1555 1555 1.73
CISPEP 1 ASP A 111 PRO A 112 0 -4.31
CRYST1 41.550 52.440 48.190 90.00 90.00 90.00 P 21 21 2 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 0.024067 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019069 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020751 0.00000