HEADER UNKNOWN FUNCTION 24-JUN-13 4LD6 TITLE PWWP DOMAIN OF HUMAN PWWP DOMAIN-CONTAINING PROTEIN 2B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PWWP DOMAIN-CONTAINING PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PWWP DOMAIN (UNP RESIDUES 475-590); 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: PWWP2B, PWWP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)V2RPRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, UNKNOWN KEYWDS 2 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.DONG,L.DOMBROVSKI,W.TEMPEL,P.LOPPNAU,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,P.J.BROWN,H.WU,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 28-FEB-24 4LD6 1 REMARK SEQADV REVDAT 1 17-JUL-13 4LD6 0 JRNL AUTH L.DOMBROVSKI,A.DONG,W.TEMPEL,P.LOPPNAU,C.BOUNTRA, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,P.J.BROWN,H.WU, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF PWWP DOMAIN OF HUMAN PWWP JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 2B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11787 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 + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 660 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 686 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 933 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 0.80000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.841 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1060 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1025 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1450 ; 1.384 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2371 ; 0.774 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 143 ; 6.325 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;27.126 ;21.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 191 ;13.251 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.178 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1203 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 265 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4LD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-13; 22-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; APS REMARK 200 BEAMLINE : NULL; 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178; 0.97944 REMARK 200 MONOCHROMATOR : VARIMAX; DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL; ADJUSTABLE FOCUSING REMARK 200 MIRRORS IN K-B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC; MARMOSAIC 300 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11827 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 56.4000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 36.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M AMMONIUM ACETATE, REMARK 280 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 16.07400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.98600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.52750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.98600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.07400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.52750 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 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 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 LYS A 552 CE NZ REMARK 470 LYS A 565 CD CE NZ 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 GLU A 517 -5.01 80.52 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 GOL A 3001 DBREF 4LD6 A 475 590 UNP Q6NUJ5 PWP2B_HUMAN 475 590 SEQADV 4LD6 GLY A 474 UNP Q6NUJ5 EXPRESSION TAG SEQRES 1 A 117 GLY GLN SER VAL SER GLU CYS ILE THR GLU ASP GLY ARG SEQRES 2 A 117 THR VAL ALA VAL GLY ASP ILE VAL TRP GLY LYS ILE HIS SEQRES 3 A 117 GLY PHE PRO TRP TRP PRO ALA ARG VAL LEU ASP ILE SER SEQRES 4 A 117 LEU GLY GLN LYS GLU ASP GLY GLU PRO SER TRP ARG GLU SEQRES 5 A 117 ALA LYS VAL SER TRP PHE GLY SER PRO THR THR SER PHE SEQRES 6 A 117 LEU SER ILE SER LYS LEU SER PRO PHE SER GLU PHE PHE SEQRES 7 A 117 LYS LEU ARG PHE ASN ARG LYS LYS LYS GLY MET TYR ARG SEQRES 8 A 117 LYS ALA ILE THR GLU ALA ALA ASN ALA ALA ARG HIS VAL SEQRES 9 A 117 ALA PRO GLU ILE ARG GLU LEU LEU THR GLN PHE GLU THR HET GOL A3001 6 HET UNX A3002 1 HET UNX A3003 1 HET UNX A3004 1 HET UNX A3005 1 HET UNX A3006 1 HET UNX A3007 1 HETNAM GOL GLYCEROL HETNAM UNX UNKNOWN ATOM OR ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 UNX 6(X) FORMUL 9 HOH *130(H2 O) HELIX 1 1 PHE A 550 PHE A 555 1 6 HELIX 2 2 GLY A 561 ALA A 574 1 14 HELIX 3 3 ALA A 578 GLU A 589 1 12 SHEET 1 A 4 GLN A 475 VAL A 477 0 SHEET 2 A 4 TRP A 504 LEU A 513 -1 O LEU A 513 N GLN A 475 SHEET 3 A 4 ARG A 524 TRP A 530 -1 O LYS A 527 N LEU A 509 SHEET 4 A 4 THR A 536 SER A 540 -1 O LEU A 539 N ALA A 526 SHEET 1 B 4 GLN A 475 VAL A 477 0 SHEET 2 B 4 TRP A 504 LEU A 513 -1 O LEU A 513 N GLN A 475 SHEET 3 B 4 ILE A 493 GLY A 496 -1 N VAL A 494 O ALA A 506 SHEET 4 B 4 LEU A 544 PRO A 546 -1 O SER A 545 N TRP A 495 SHEET 1 C 2 GLU A 479 ILE A 481 0 SHEET 2 C 2 THR A 487 ALA A 489 -1 O VAL A 488 N CYS A 480 SITE 1 AC1 8 ILE A 498 PHE A 501 TRP A 504 TRP A 530 SITE 2 AC1 8 SER A 533 MET A 562 HOH A3101 HOH A3139 CRYST1 32.148 41.055 77.972 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 0.031106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012825 0.00000