10 20 30 40 50 60 70 80 1ZLM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER SIGNALING PROTEIN 06-MAY-05 1ZLM
TITLE CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF HUMAN OSTEOCLAST TITLE 2 STIMULATING FACTOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSTEOCLAST STIMULATING FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 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: OSTF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-OSF-SH3
KEYWDS BETA BARREL, SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR L.CHEN,Y.WANG,D.WELLS,D.TOH,H.HAROLD,J.ZHOU,E.DIGIAMMARINO, AUTHOR 2 E.J.MEEHAN
REVDAT 3 24-FEB-09 1ZLM 1 VERSN REVDAT 2 05-SEP-06 1ZLM 1 JRNL REVDAT 1 16-MAY-06 1ZLM 0
JRNL AUTH L.CHEN,Y.WANG,D.WELLS,D.TOH,H.HAROLD,J.ZHOU, JRNL AUTH 2 E.DIGIAMMARINO,E.J.MEEHAN JRNL TITL STRUCTURE OF THE SH3 DOMAIN OF HUMAN JRNL TITL 2 OSTEOCLAST-STIMULATING FACTOR AT ATOMIC RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 62 844 2006 JRNL REFN ESSN 1744-3091 JRNL PMID 16946461 JRNL DOI 10.1107/S1744309106030004
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.158 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1333 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27365 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.153 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 23025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 607.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5467 REMARK 3 NUMBER OF RESTRAINTS : 6382 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.090 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.045 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.082 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) BY 5%
REMARK 4 REMARK 4 1ZLM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-05. REMARK 100 THE RCSB ID CODE IS RCSB032862.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27403 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 31.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : 0.09800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : 0.24100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: 1GRI REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM HEPES, PEG400, AMMONIUM REMARK 280 SULFATE, PH 7.5, TEMPERATURE 277K, VAPOR DIFFUSION, SITTING REMARK 280 DROP
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 24.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 18.40500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.24000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.40500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.24000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.58000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.40500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.24000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 24.58000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.40500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.24000 REMARK 290 SMTRY3 8 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS ONE MONOMER WHICH IS THE REMARK 300 BIOLOGICAL UNIT.
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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 198 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 201 LIES ON A SPECIAL POSITION.
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 ASP A 43 CB - CG - OD1 ANGL. DEV. = 6.4 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 218 DISTANCE = 7.22 ANGSTROMS
DBREF 1ZLM A 12 69 UNP Q92882 OSTF1_HUMAN 12 69
SEQRES 1 A 58 GLY GLN VAL LYS VAL PHE ARG ALA LEU TYR THR PHE GLU SEQRES 2 A 58 PRO ARG THR PRO ASP GLU LEU TYR PHE GLU GLU GLY ASP SEQRES 3 A 58 ILE ILE TYR ILE THR ASP MET SER ASP THR ASN TRP TRP SEQRES 4 A 58 LYS GLY THR SER LYS GLY ARG THR GLY LEU ILE PRO SER SEQRES 5 A 58 ASN TYR VAL ALA GLU GLN
FORMUL 2 HOH *130(H2 O)
SHEET 1 A 5 ARG A 57 PRO A 62 0 SHEET 2 A 5 TRP A 49 SER A 54 -1 N TRP A 50 O ILE A 61 SHEET 3 A 5 ILE A 38 ASP A 43 -1 N TYR A 40 O THR A 53 SHEET 4 A 5 LYS A 15 ALA A 19 -1 N LYS A 15 O ILE A 41 SHEET 5 A 5 VAL A 66 GLU A 68 -1 O ALA A 67 N ARG A 18
CRYST1 36.810 80.480 49.160 90.00 90.00 90.00 C 2 2 21 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 0.027167 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012425 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020342 0.00000