HEADER PROTEIN BINDING 10-JUL-13 4LMM TITLE CRYSTAL STRUCTURE OF NHERF1 PDZ1 DOMAIN COMPLEXED WITH THE CXCR2 C- TITLE 2 TERMINAL TAIL IN P21 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NA(+)/H(+) EXCHANGE REGULATORY COFACTOR NHE-RF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 11-95; 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: NHERF, NHERF1, SLC9A3R1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PSUMO KEYWDS CXCR2, NHERF1, NEUTROPHIL, INFLAMMATORY DISEASES, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIANG,G.LU,Y.WU,J.BRUNZELLE,N.SIRINUPONG,C.LI,Z.YANG REVDAT 2 20-SEP-23 4LMM 1 REMARK SEQADV REVDAT 1 15-JAN-14 4LMM 0 JRNL AUTH Y.JIANG,G.LU,L.R.TRESCOTT,Y.HOU,X.GUAN,S.WANG, JRNL AUTH 2 A.STAMENKOVICH,J.BRUNZELLE,N.SIRINUPONG,C.LI,Z.YANG JRNL TITL NEW CONFORMATIONAL STATE OF NHERF1-CXCR2 SIGNALING COMPLEX JRNL TITL 2 CAPTURED BY CRYSTAL LATTICE TRAPPING. JRNL REF PLOS ONE V. 8 81904 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24339979 JRNL DOI 10.1371/JOURNAL.PONE.0081904 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 29864 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1503 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 : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.86 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2434 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2070 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2318 REMARK 3 BIN R VALUE (WORKING SET) : 0.2071 REMARK 3 BIN FREE R VALUE : 0.2056 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.77 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 116 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 : 691 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09220 REMARK 3 B22 (A**2) : -0.19690 REMARK 3 B33 (A**2) : 0.10470 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.23100 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.145 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.037 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 737 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1005 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 274 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 20 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 115 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 737 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 92 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 918 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.07 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.31 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: A 9 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): -12.3646 -16.3611 -23.5356 REMARK 3 T TENSOR REMARK 3 T11: -0.0477 T22: -0.0359 REMARK 3 T33: -0.0287 T12: 0.0063 REMARK 3 T13: -0.0064 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 1.1845 L22: 1.2396 REMARK 3 L33: 0.6397 L12: -0.3841 REMARK 3 L13: -0.3953 L23: 0.4564 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: 0.0515 S13: -0.0465 REMARK 3 S21: -0.0039 S22: -0.0617 S23: 0.0565 REMARK 3 S31: 0.0282 S32: -0.0111 S33: 0.0595 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000080819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : KOHZU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30032 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.02400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4JL7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, 0.2 M AMMONIUM REMARK 280 ACETATE, 24% PEG4000, PH 4.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.75450 REMARK 290 SMTRY3 2 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: MONOMERIC 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 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 LYS A 32 97.02 79.49 REMARK 500 ASN A 84 11.98 -141.65 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 ACY A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 102 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE FIVE RESIDUES MIMIC THE C-TERMINAL TAIL OF CXCR2. DBREF 4LMM A 11 94 UNP O14745 NHRF1_HUMAN 11 94 SEQADV 4LMM GLY A 9 UNP O14745 EXPRESSION TAG SEQADV 4LMM MET A 10 UNP O14745 EXPRESSION TAG SEQADV 4LMM THR A 95 UNP O14745 SEE REMARK 999 SEQADV 4LMM SER A 96 UNP O14745 SEE REMARK 999 SEQADV 4LMM THR A 97 UNP O14745 SEE REMARK 999 SEQADV 4LMM THR A 98 UNP O14745 SEE REMARK 999 SEQADV 4LMM LEU A 99 UNP O14745 SEE REMARK 999 SEQRES 1 A 91 GLY MET LEU PRO ARG LEU CYS CYS LEU GLU LYS GLY PRO SEQRES 2 A 91 ASN GLY TYR GLY PHE HIS LEU HIS GLY GLU LYS GLY LYS SEQRES 3 A 91 LEU GLY GLN TYR ILE ARG LEU VAL GLU PRO GLY SER PRO SEQRES 4 A 91 ALA GLU LYS ALA GLY LEU LEU ALA GLY ASP ARG LEU VAL SEQRES 5 A 91 GLU VAL ASN GLY GLU ASN VAL GLU LYS GLU THR HIS GLN SEQRES 6 A 91 GLN VAL VAL SER ARG ILE ARG ALA ALA LEU ASN ALA VAL SEQRES 7 A 91 ARG LEU LEU VAL VAL ASP PRO GLU THR SER THR THR LEU HET ACY A 101 4 HET CL A 102 1 HETNAM ACY ACETIC ACID HETNAM CL CHLORIDE ION FORMUL 2 ACY C2 H4 O2 FORMUL 3 CL CL 1- FORMUL 4 HOH *129(H2 O) HELIX 1 1 SER A 46 ALA A 51 1 6 HELIX 2 2 THR A 71 ALA A 82 1 12 SHEET 1 A 4 ARG A 13 GLU A 18 0 SHEET 2 A 4 ALA A 85 VAL A 91 -1 O LEU A 88 N CYS A 15 SHEET 3 A 4 ARG A 58 VAL A 62 -1 N VAL A 60 O LEU A 89 SHEET 4 A 4 GLU A 65 ASN A 66 -1 O GLU A 65 N VAL A 62 SHEET 1 B 2 HIS A 27 GLY A 30 0 SHEET 2 B 2 GLN A 37 ARG A 40 -1 O TYR A 38 N HIS A 29 SITE 1 AC1 5 GLY A 20 PRO A 21 ARG A 58 LYS A 69 SITE 2 AC1 5 HOH A 234 SITE 1 AC2 6 GLY A 56 ARG A 58 VAL A 91 ASP A 92 SITE 2 AC2 6 PRO A 93 HOH A 277 CRYST1 26.593 45.509 33.446 90.00 109.71 90.00 P 1 21 1 2 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 0.037604 0.000000 0.013472 0.00000 SCALE2 0.000000 0.021974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031760 0.00000