HEADER UNKNOWN FUNCTION 19-MAR-04 1SQW TITLE CRYSTAL STRUCTURE OF KD93, A NOVEL PROTEIN EXPRESSED IN THE HUMAN PRO COMPND MOL_ID: 1; COMPND 2 MOLECULE: SACCHAROMYCES CEREVISIAE NIP7P HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: NOVEL PROTEIN EXPRESSED IN HUMAN HEMATOPOIETIC COMPND 6 STEM/PROGENITOR CELLS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NOVEL GENE; 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: PET22B; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-KD93 KEYWDS PUA, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.F.LIU,X.Q.WANG,Z.X.WANG,J.R.CHEN,T.JIANG,X.M.AN,W.R.CHAN,D.C.LIANG REVDAT 3 14-FEB-24 1SQW 1 SEQADV REVDAT 2 24-FEB-09 1SQW 1 VERSN REVDAT 1 22-MAR-05 1SQW 0 JRNL AUTH J.F.LIU,X.Q.WANG,Z.X.WANG,J.R.CHEN,T.JIANG,X.M.AN,W.R.CHANG, JRNL AUTH 2 D.C.LIANG JRNL TITL CRYSTAL STRUCTURE OF KD93, A NOVEL PROTEIN EXPRESSED IN JRNL TITL 2 HUMAN HEMATOPOIETIC STEM/PROGENITOR CELLS. JRNL REF J.STRUCT.BIOL. V. 148 370 2004 JRNL REFN ISSN 1047-8477 JRNL PMID 15522784 JRNL DOI 10.1016/J.JSB.2004.06.010 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1409 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 131 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) : 0.16300 REMARK 3 B22 (A**2) : 0.16300 REMARK 3 B33 (A**2) : -0.32700 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) : 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.418 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021933. 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 : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793, 0.9799, 0.9712 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17749 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 4000, 0.2M MGCL2, 0.1M SODIUM REMARK 280 ACETATE BUFFER, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 66.02400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.60150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.60150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.01200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.60150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.60150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 99.03600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.60150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.60150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.01200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.60150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.60150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 99.03600 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 66.02400 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 GLU A 177 REMARK 465 THR A 178 REMARK 465 LEU A 179 REMARK 465 THR A 180 REMARK 465 LEU A 181 REMARK 465 GLU A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 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 ASP A 42 -4.63 66.04 REMARK 500 TYR A 172 -32.20 -142.88 REMARK 500 VAL A 173 31.14 -67.65 REMARK 500 ARG A 174 0.35 -56.79 REMARK 500 HIS A 175 1.03 91.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 1SQW A 1 180 UNP Q9Y221 NIP7_HUMAN 1 180 SEQADV 1SQW LEU A 181 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW GLU A 182 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 183 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 184 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 185 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 186 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 187 UNP Q9Y221 CLONING ARTIFACT SEQADV 1SQW HIS A 188 UNP Q9Y221 CLONING ARTIFACT SEQRES 1 A 188 MET ARG PRO LEU THR GLU GLU GLU THR ARG VAL MET PHE SEQRES 2 A 188 GLU LYS ILE ALA LYS TYR ILE GLY GLU ASN LEU GLN LEU SEQRES 3 A 188 LEU VAL ASP ARG PRO ASP GLY THR TYR CYS PHE ARG LEU SEQRES 4 A 188 HIS ASN ASP ARG VAL TYR TYR VAL SER GLU LYS ILE MET SEQRES 5 A 188 LYS LEU ALA ALA ASN ILE SER GLY ASP LYS LEU VAL SER SEQRES 6 A 188 LEU GLY THR CYS PHE GLY LYS PHE THR LYS THR HIS LYS SEQRES 7 A 188 PHE ARG LEU HIS VAL THR ALA LEU ASP TYR LEU ALA PRO SEQRES 8 A 188 TYR ALA LYS TYR LYS VAL TRP ILE LYS PRO GLY ALA GLU SEQRES 9 A 188 GLN SER PHE LEU TYR GLY ASN HIS VAL LEU LYS SER GLY SEQRES 10 A 188 LEU GLY ARG ILE THR GLU ASN THR SER GLN TYR GLN GLY SEQRES 11 A 188 VAL VAL VAL TYR SER MET ALA ASP ILE PRO LEU GLY PHE SEQRES 12 A 188 GLY VAL ALA ALA LYS SER THR GLN ASP CYS ARG LYS VAL SEQRES 13 A 188 ASP PRO MET ALA ILE VAL VAL PHE HIS GLN ALA ASP ILE SEQRES 14 A 188 GLY GLU TYR VAL ARG HIS GLU GLU THR LEU THR LEU GLU SEQRES 15 A 188 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *131(H2 O) HELIX 1 1 THR A 5 GLY A 21 1 17 HELIX 2 2 LEU A 24 VAL A 28 1 5 HELIX 3 3 GLU A 49 LEU A 54 1 6 HELIX 4 4 SER A 59 GLY A 67 1 9 HELIX 5 5 ALA A 85 ALA A 90 1 6 HELIX 6 6 PRO A 91 ALA A 93 5 3 HELIX 7 7 LYS A 100 LEU A 108 1 9 HELIX 8 8 SER A 149 VAL A 156 1 8 HELIX 9 9 GLY A 170 TYR A 172 5 3 SHEET 1 A 3 ARG A 2 PRO A 3 0 SHEET 2 A 3 GLY A 33 HIS A 40 -1 O LEU A 39 N ARG A 2 SHEET 3 A 3 ASP A 29 ARG A 30 -1 O ARG A 30 N GLY A 33 SHEET 1 B 5 ARG A 2 PRO A 3 0 SHEET 2 B 5 GLY A 33 HIS A 40 -1 O LEU A 39 N ARG A 2 SHEET 3 B 5 ARG A 43 SER A 48 -1 O VAL A 47 N CYS A 36 SHEET 4 B 5 THR A 68 PHE A 73 -1 O THR A 68 N TYR A 46 SHEET 5 B 5 PHE A 79 LEU A 81 -1 O ARG A 80 N LYS A 72 SHEET 1 C 6 VAL A 113 LEU A 114 0 SHEET 2 C 6 ILE A 161 ASP A 168 -1 O VAL A 162 N VAL A 113 SHEET 3 C 6 PRO A 140 ALA A 146 -1 N VAL A 145 O PHE A 164 SHEET 4 C 6 GLY A 130 SER A 135 -1 N VAL A 133 O LEU A 141 SHEET 5 C 6 LYS A 96 ILE A 99 1 N ILE A 99 O TYR A 134 SHEET 6 C 6 LEU A 118 ILE A 121 -1 O ARG A 120 N TRP A 98 CRYST1 57.203 57.203 132.048 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 0.017482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007573 0.00000