HEADER STRUCTURAL PROTEIN 12-SEP-13 4MPA TITLE CRYSTAL STRUCTURE OF NHERF1-CXCR2 SIGNALING COMPLEX IN P21 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NA(+)/H(+) EXCHANGE REGULATORY COFACTOR NHE-RF1, C-X-C COMPND 3 CHEMOKINE RECEPTOR TYPE 2 CHIMERA; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SEE REMARK 999; COMPND 6 SYNONYM: NHERF-1, EZRIN-RADIXIN-MOESIN-BINDING PHOSPHOPROTEIN 50, COMPND 7 EBP50, REGULATORY COFACTOR OF NA(+)/H(+) EXCHANGER, SODIUM-HYDROGEN COMPND 8 EXCHANGER REGULATORY FACTOR 1, SOLUTE CARRIER FAMILY 9 ISOFORM A3 COMPND 9 REGULATORY FACTOR 1, CXC-R2, CXCR-2, CDW128B, GRO/MGSA RECEPTOR, HIGH COMPND 10 AFFINITY INTERLEUKIN-8 RECEPTOR B, IL-8R B, L-8 RECEPTOR TYPE 2; COMPND 11 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, CXCR2; 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 NEUTROPHIL, INFLAMMATORY DISEASES, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIANG,G.LU,Y.WU,J.BRUNZELLE,N.SIRINUPONG,C.LI,Z.YANG REVDAT 3 20-SEP-23 4MPA 1 REMARK SEQADV REVDAT 2 28-JUN-17 4MPA 1 DBREF REVDAT 1 15-JAN-14 4MPA 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 : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML 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 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 30006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.9001 - 2.4400 0.97 2633 153 0.1691 0.1672 REMARK 3 2 2.4400 - 1.9369 1.00 2653 150 0.1443 0.1610 REMARK 3 3 1.9369 - 1.6921 1.00 2638 149 0.1356 0.1583 REMARK 3 4 1.6921 - 1.5375 1.00 2669 141 0.1241 0.1460 REMARK 3 5 1.5375 - 1.4273 1.00 2671 130 0.1200 0.1280 REMARK 3 6 1.4273 - 1.3431 1.00 2611 137 0.1196 0.1403 REMARK 3 7 1.3431 - 1.2759 1.00 2641 158 0.1177 0.1388 REMARK 3 8 1.2759 - 1.2203 1.00 2653 126 0.1193 0.1354 REMARK 3 9 1.2203 - 1.1733 1.00 2635 130 0.1237 0.1569 REMARK 3 10 1.1733 - 1.1329 0.97 2593 129 0.1380 0.1622 REMARK 3 11 1.1329 - 1.0970 0.80 2101 105 0.1580 0.1928 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 731 REMARK 3 ANGLE : 1.425 995 REMARK 3 CHIRALITY : 0.065 115 REMARK 3 PLANARITY : 0.005 133 REMARK 3 DIHEDRAL : 13.239 288 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082195. 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 : DIAMOND(111) 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) : 1.097 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, PH 4.8, 0.2 M REMARK 280 AMMONIUM ACETATE, 24% PEG4000, 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 94 O HOH A 290 2.00 REMARK 500 O HOH A 230 O HOH A 348 2.05 REMARK 500 O HOH A 212 O HOH A 348 2.07 REMARK 500 O HOH A 310 O HOH A 329 2.10 REMARK 500 OE2 GLU A 31 O HOH A 311 2.11 REMARK 500 O HOH A 220 O HOH A 311 2.17 REMARK 500 O HOH A 324 O HOH A 358 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 18 O HOH A 319 2353 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 -70.32 -62.51 REMARK 500 ASN A 84 16.11 -142.57 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 PROTEIN IS A CHIMERA OF RESIDUES 11-95 OF PDZ DOMAIN OF NHERF1 AND REMARK 999 RESIDUES 356-360 OF CXCR2 (RESIDUE 95 OF NHERF1 AND RESIDUE 356 OF REMARK 999 CXCR2 ARE THE SAME RESIDUE). DBREF 4MPA A 11 94 UNP O14745 NHRF1_HUMAN 11 94 DBREF 4MPA A 95 99 UNP P25025 CXCR2_HUMAN 356 360 SEQADV 4MPA GLY A 9 UNP O14745 EXPRESSION TAG SEQADV 4MPA MET A 10 UNP O14745 EXPRESSION TAG 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 7 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 *158(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 HIS A 29 0 SHEET 2 B 2 TYR A 38 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 230 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 273 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